rs7315621

Variant names:

• chr12-131600651-G-A
• rs7315621

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.414 in 151,974 control chromosomes in the GnomAD database, including 13,271 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 0.41 (13271 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62913 AN: 151856 Hom.: 13264 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.414 AC: 62942 AN: 151974 Hom.: 13271 Cov.: 32 AF XY: 0.410 AC XY: 30421 AN XY: 74252

African (AFR) AF: 0.377 AC: 15641 AN: 41452

American (AMR) AF: 0.430 AC: 6581 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1797 AN: 3470

East Asian (EAS) AF: 0.398 AC: 2045 AN: 5140

South Asian (SAS) AF: 0.386 AC: 1856 AN: 4808

European-Finnish (FIN) AF: 0.337 AC: 3553 AN: 10552

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29923 AN: 67936

Other (OTH) AF: 0.448 AC: 946 AN: 2112

Alfa AF: 0.435 Hom.: 28319

Bravo AF: 0.425

Asia WGS AF: 0.368 AC: 1280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.27
DANN	Benign	0.41
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs7315621; hg19: chr12-132085196;