Genetic Variant LOC105375040:n.296-2205T>C (chr6-37336610-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XR_007059566.1(LOC105375040):n.296-2205T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 151,624 control chromosomes in the GnomAD database, including 9,500 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 0.33 ( 9500 hom., cov: 32)

Consequence

LOC105375040
XR_007059566.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.05

Publications

3 publications found

Variant links:

Genes affected

LOC105375040 (HGNC:):

LOC105375040 links:

Genome browser will be placed here

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=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375040	XR_007059566.1 link	n.296-2205T>C		intron_variant	Intron 2 of 3
LOC105375040	XR_926762.3 link	n.296-2205T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.332

AC:

50244

AN:

151508

Hom.:

9481

Cov.:

show subpopulations

Gnomad AFR

AF:

0.517

Gnomad AMI

AF:

0.295

Gnomad AMR

AF:

0.332

Gnomad ASJ

AF:

0.296

Gnomad EAS

AF:

0.120

Gnomad SAS

AF:

0.204

Gnomad FIN

AF:

0.353

Gnomad MID

AF:

0.239

Gnomad NFE

AF:

0.244

Gnomad OTH

AF:

0.327

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.332

AC:

50317

AN:

151624

Hom.:

9500

Cov.:

AF XY:

0.332

AC XY:

24604

AN XY:

74066

show subpopulations

African (AFR)

AF:

0.517

AC:

21371

AN:

41328

American (AMR)

AF:

0.332

AC:

5052

AN:

15218

Ashkenazi Jewish (ASJ)

AF:

0.296

AC:

1028

AN:

3468

East Asian (EAS)

AF:

0.120

AC:

618

AN:

5154

South Asian (SAS)

AF:

0.204

AC:

979

AN:

4796

European-Finnish (FIN)

AF:

0.353

AC:

3698

AN:

10470

Middle Eastern (MID)

AF:

0.260

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.244

AC:

16546

AN:

67888

Other (OTH)

AF:

0.324

AC:

682

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1580

3160

4740

6320

7900

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

468

936

1404

1872

2340

<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:

0.270

Hom.:

6388

Bravo

AF:

0.343

Asia WGS

AF:

0.218

AC:

759

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.7

(source)

DANN

Benign

0.49

PhyloP100

-1.1

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over