dbSNP rs62421103: LOC107986634:n.59+7620C>A (chr6-112839142-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XR_001744300.1(LOC107986634):n.59+7620C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0429 in 152,142 control chromosomes in the GnomAD database, including 212 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 0.043 ( 212 hom., cov: 32)

Consequence

LOC107986634
XR_001744300.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.217

Publications

0 publications found

Variant links:

Genes affected

LOC107986634 (HGNC:):

LOC107986634 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=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0617 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC107986634	XR_001744300.1 link	n.59+7620C>A	intron_variant	Intron 1 of 6
LOC107986634	XR_001744301.2 link	n.59+7620C>A	intron_variant	Intron 1 of 5
LOC107986634	XR_001744302.1 link	n.59+7620C>A	intron_variant	Intron 1 of 6
LOC107986634	XR_001744303.1 link	n.59+7620C>A	intron_variant	Intron 1 of 5

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.0430

AC:

6532

AN:

152026

Hom.:

211

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00997

Gnomad AMI

AF:

0.0318

Gnomad AMR

AF:

0.0319

Gnomad ASJ

AF:

0.0332

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00767

Gnomad FIN

AF:

0.100

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0633

Gnomad OTH

AF:

0.0392

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

GnomAD4 genome

AF:

0.0429

AC:

6529

AN:

152142

Hom.:

212

Cov.:

AF XY:

0.0436

AC XY:

3245

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.00994

AC:

413

AN:

41538

American (AMR)

AF:

0.0318

AC:

486

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.0332

AC:

115

AN:

3464

East Asian (EAS)

AF:

0.000194

AC:

AN:

5156

South Asian (SAS)

AF:

0.00788

AC:

AN:

4820

European-Finnish (FIN)

AF:

0.100

AC:

1061

AN:

10576

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0633

AC:

4303

AN:

67986

Other (OTH)

AF:

0.0388

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

313

626

939

1252

1565

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

148

222

296

370

<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:

0.0515

Hom.:

Bravo

AF:

0.0360

Asia WGS

AF:

0.00491

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.1

(source)

DANN

Benign

0.32

PhyloP100

-0.22

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