Genetic Variant LOC105376810:n.333G>A (chr2-241227135-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XR_001739176.3(LOC105376810):n.333G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.733 in 152,264 control chromosomes in the GnomAD database, including 42,097 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.73 ( 42042 hom., cov: 31)

Exomes 𝑓: 0.84 ( 55 hom. )

Consequence

LOC105376810
XR_001739176.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.09

Publications

9 publications found

Variant links:

Genes affected

LOC105376810 (HGNC:):

LOC105376810 links:

ANO7 (HGNC:31677): (anoctamin 7) This prostate-specific gene encodes a cytoplasmic protein, as well as a polytopic membrane protein which may serve as a target in prostate cancer diagnosis and immunotherapy. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Aug 2011]

ANO7 links:

HDLBP (HGNC:4857): (high density lipoprotein binding protein) The protein encoded by this gene binds high density lipoprotein (HDL) and may function to regulate excess cholesterol levels in cells. The encoded protein also binds RNA and can induce heterochromatin formation. [provided by RefSeq, Mar 2016]

HDLBP links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000310931.10. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
HDLBP	NM_005336.6	MANE Select	c.*2466C>T	downstream_gene	N/A	NP_005327.1
HDLBP	NM_001320965.3		c.*2466C>T	downstream_gene	N/A	NP_001307894.1
HDLBP	NM_001320966.3		c.*2466C>T	downstream_gene	N/A	NP_001307895.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
HDLBP	ENST00000310931.10	TSL:1 MANE Select	c.*2466C>T	downstream_gene	N/A	ENSP00000312042.4
HDLBP	ENST00000391975.5	TSL:1	c.*2466C>T	downstream_gene	N/A	ENSP00000375836.1
HDLBP	ENST00000427183.6	TSL:2	c.*2466C>T	downstream_gene	N/A	ENSP00000399139.2

Frequencies

GnomAD3 genomes

AF:

0.732

AC:

111316

AN:

151988

Hom.:

42007

Cov.:

show subpopulations

Gnomad AFR

AF:

0.540

Gnomad AMI

AF:

0.845

Gnomad AMR

AF:

0.832

Gnomad ASJ

AF:

0.840

Gnomad EAS

AF:

0.949

Gnomad SAS

AF:

0.706

Gnomad FIN

AF:

0.829

Gnomad MID

AF:

0.835

Gnomad NFE

AF:

0.788

Gnomad OTH

AF:

0.780

GnomAD4 exome

AF:

0.835

AC:

132

AN:

158

Hom.:

AF XY:

0.854

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.856

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.793

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.732

AC:

111403

AN:

152106

Hom.:

42042

Cov.:

AF XY:

0.740

AC XY:

54993

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.540

AC:

22373

AN:

41452

American (AMR)

AF:

0.832

AC:

12723

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.840

AC:

2915

AN:

3472

East Asian (EAS)

AF:

0.949

AC:

4908

AN:

5170

South Asian (SAS)

AF:

0.707

AC:

3408

AN:

4820

European-Finnish (FIN)

AF:

0.829

AC:

8792

AN:

10600

Middle Eastern (MID)

AF:

0.850

AC:

250

AN:

294

European-Non Finnish (NFE)

AF:

0.788

AC:

53614

AN:

67996

Other (OTH)

AF:

0.783

AC:

1651

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1435

2870

4304

5739

7174

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

836

1672

2508

3344

4180

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.781

Hom.:

59136

Bravo

AF:

0.729

Asia WGS

AF:

0.828

AC:

2879

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.026

(source)

DANN

Benign

0.30

PhyloP100

-4.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over