rs1437869

Variant names:

• chr2-196960257-A-C
• rs1437869

Your query was ambiguous. Multiple possible variants found:

• chr2-196960257-A-C
• chr2-196960257-A-G

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 0.9 in 151,964 control chromosomes in the GnomAD database, including 63,291 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 0.90 (63291 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 1 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 = 0.992 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: 0.900 AC: 136657 AN: 151846 Hom.: 63261 Cov.: 29

Gnomad AFR AF: 0.655

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.958

Gnomad ASJ AF: 0.995

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.998

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.932

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

GnomAD4 genome AF: 0.900 AC: 136739 AN: 151964 Hom.: 63291 Cov.: 29 AF XY: 0.904 AC XY: 67132 AN XY: 74294

African (AFR) AF: 0.655 AC: 27093 AN: 41370

American (AMR) AF: 0.958 AC: 14604 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.995 AC: 3451 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5170 AN: 5170

South Asian (SAS) AF: 0.999 AC: 4811 AN: 4818

European-Finnish (FIN) AF: 1.00 AC: 10584 AN: 10584

Middle Eastern (MID) AF: 0.990 AC: 291 AN: 294

European-Non Finnish (NFE) AF: 0.998 AC: 67854 AN: 67986

Other (OTH) AF: 0.933 AC: 1969 AN: 2110

Alfa AF: 0.838 Hom.: 17464

Bravo AF: 0.887

Asia WGS AF: 0.977 AC: 3400 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	0.54
DANN	Benign	0.74
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1437869; hg19: chr2-197824981;