Genetic Variant LOC105373691:n.194-702A>C (chr2-153027501-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XR_007087267.1(LOC105373691):n.194-702A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 151,824 control chromosomes in the GnomAD database, including 9,684 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 0.34 ( 9684 hom., cov: 31)

Consequence

LOC105373691
XR_007087267.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.02

Publications

4 publications found

Variant links:

Genes affected

LOC105373691 (HGNC:):

LOC105373691 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=-0.48).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105373691	XR_007087267.1 link	n.194-702A>C	intron_variant	Intron 2 of 3
LOC105373691	XR_007087268.1 link	n.130-702A>C	intron_variant	Intron 2 of 3
LOC105373691	XR_923481.1 link	n.310-702A>C	intron_variant	Intron 3 of 3
LOC105373691	XR_923482.2 link	n.246-702A>C	intron_variant	Intron 3 of 3

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.341

AC:

51731

AN:

151706

Hom.:

9682

Cov.:

show subpopulations

Gnomad AFR

AF:

0.194

Gnomad AMI

AF:

0.331

Gnomad AMR

AF:

0.340

Gnomad ASJ

AF:

0.328

Gnomad EAS

AF:

0.185

Gnomad SAS

AF:

0.372

Gnomad FIN

AF:

0.340

Gnomad MID

AF:

0.335

Gnomad NFE

AF:

0.441

Gnomad OTH

AF:

0.342

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

GnomAD4 genome

AF:

0.341

AC:

51750

AN:

151824

Hom.:

9684

Cov.:

AF XY:

0.335

AC XY:

24860

AN XY:

74210

show subpopulations

African (AFR)

AF:

0.194

AC:

8031

AN:

41422

American (AMR)

AF:

0.340

AC:

5174

AN:

15218

Ashkenazi Jewish (ASJ)

AF:

0.328

AC:

1136

AN:

3468

East Asian (EAS)

AF:

0.186

AC:

961

AN:

5170

South Asian (SAS)

AF:

0.372

AC:

1789

AN:

4814

European-Finnish (FIN)

AF:

0.340

AC:

3579

AN:

10528

Middle Eastern (MID)

AF:

0.354

AC:

104

AN:

294

European-Non Finnish (NFE)

AF:

0.441

AC:

29959

AN:

67884

Other (OTH)

AF:

0.338

AC:

715

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1654

3309

4963

6618

8272

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

518

1036

1554

2072

2590

<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:

0.352

Hom.:

6175

Bravo

AF:

0.330

Asia WGS

AF:

0.262

AC:

910

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

8.5

(source)

DANN

Benign

0.95

PhyloP100

3.0

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