rs1437683

Variant names:

• chr2-118541311-G-A
• rs1437683

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 0.501 in 152,084 control chromosomes in the GnomAD database, including 19,496 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 0.50 (19496 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.602 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: 0.501 AC: 76162 AN: 151966 Hom.: 19469 Cov.: 33

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.501 AC: 76238 AN: 152084 Hom.: 19496 Cov.: 33 AF XY: 0.497 AC XY: 36947 AN XY: 74332

African (AFR) AF: 0.608 AC: 25227 AN: 41492

American (AMR) AF: 0.517 AC: 7900 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1381 AN: 3468

East Asian (EAS) AF: 0.394 AC: 2040 AN: 5178

South Asian (SAS) AF: 0.349 AC: 1680 AN: 4818

European-Finnish (FIN) AF: 0.467 AC: 4925 AN: 10552

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.462 AC: 31411 AN: 67966

Other (OTH) AF: 0.482 AC: 1019 AN: 2116

Alfa AF: 0.472 Hom.: 73179

Bravo AF: 0.512

Asia WGS AF: 0.381 AC: 1325 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.031
DANN	Benign	0.44
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs1437683; hg19: chr2-119298887; COSMIC: COSV60100368;