2-637830-A-G

Variant names:

• chr2-637830-A-G
• rs13393304

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 0.852 in 152,194 control chromosomes in the GnomAD database, including 55,315 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 0.85 (55315 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.852 AC: 129527 AN: 152076 Hom.: 55271 Cov.: 32

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.869

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.850

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.843

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

GnomAD4 genome AF: 0.852 AC: 129628 AN: 152194 Hom.: 55315 Cov.: 32 AF XY: 0.854 AC XY: 63539 AN XY: 74398

African (AFR) AF: 0.887 AC: 36840 AN: 41512

American (AMR) AF: 0.869 AC: 13298 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2549 AN: 3472

East Asian (EAS) AF: 0.919 AC: 4747 AN: 5168

South Asian (SAS) AF: 0.860 AC: 4145 AN: 4820

European-Finnish (FIN) AF: 0.849 AC: 8988 AN: 10590

Middle Eastern (MID) AF: 0.839 AC: 245 AN: 292

European-Non Finnish (NFE) AF: 0.828 AC: 56313 AN: 68010

Other (OTH) AF: 0.844 AC: 1785 AN: 2114

Alfa AF: 0.853 Hom.: 16850

Bravo AF: 0.854

Asia WGS AF: 0.893 AC: 3109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.35
PhyloP100		-0.083

Splicing

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

Other links and lift over

dbSNP: rs13393304; hg19: chr2-637830;