rs3099624

Variant names:

• chr1-11436937-C-T
• rs3099624

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 0.343 in 151,894 control chromosomes in the GnomAD database, including 10,907 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 (10907 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52147 AN: 151774 Hom.: 10908 Cov.: 31

Gnomad AFR AF: 0.0947

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.343 AC: 52136 AN: 151894 Hom.: 10907 Cov.: 31 AF XY: 0.346 AC XY: 25664 AN XY: 74234

African (AFR) AF: 0.0944 AC: 3910 AN: 41416

American (AMR) AF: 0.472 AC: 7209 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1510 AN: 3468

East Asian (EAS) AF: 0.312 AC: 1610 AN: 5154

South Asian (SAS) AF: 0.242 AC: 1164 AN: 4812

European-Finnish (FIN) AF: 0.485 AC: 5113 AN: 10544

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.447 AC: 30364 AN: 67930

Other (OTH) AF: 0.359 AC: 754 AN: 2100

Alfa AF: 0.368 Hom.: 11134

Bravo AF: 0.335

Asia WGS AF: 0.228 AC: 794 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.24
DANN	Benign	0.80
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs3099624; hg19: chr1-11496994;