rs2993410

Variant names:

• chr1-46746337-G-A
• rs2993410

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 0.687 in 152,032 control chromosomes in the GnomAD database, including 38,837 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 0.69 (38837 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.710
• Publications: 9 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 (NFE) allele frequency at 95% confidence interval = 0.846 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: 0.687 AC: 104337 AN: 151914 Hom.: 38828 Cov.: 31

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.852

Gnomad OTH AF: 0.707

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

GnomAD4 genome AF: 0.687 AC: 104372 AN: 152032 Hom.: 38837 Cov.: 31 AF XY: 0.680 AC XY: 50513 AN XY: 74324

African (AFR) AF: 0.459 AC: 19020 AN: 41424

American (AMR) AF: 0.653 AC: 9975 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2812 AN: 3470

East Asian (EAS) AF: 0.136 AC: 702 AN: 5168

South Asian (SAS) AF: 0.582 AC: 2799 AN: 4812

European-Finnish (FIN) AF: 0.825 AC: 8725 AN: 10582

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.852 AC: 57889 AN: 67982

Other (OTH) AF: 0.699 AC: 1477 AN: 2112

Alfa AF: 0.787 Hom.: 145714

Bravo AF: 0.662

Asia WGS AF: 0.362 AC: 1262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.58
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs2993410; hg19: chr1-47212009;