rs1916141

Variant names:

• chr2-57287706-C-A
• rs1916141

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 0.139 in 152,004 control chromosomes in the GnomAD database, including 1,913 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 0.14 (1913 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.620
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.352 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: 0.139 AC: 21060 AN: 151884 Hom.: 1910 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0759

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.0822

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.139 AC: 21071 AN: 152004 Hom.: 1913 Cov.: 32 AF XY: 0.143 AC XY: 10624 AN XY: 74274

African (AFR) AF: 0.227 AC: 9393 AN: 41430

American (AMR) AF: 0.0757 AC: 1157 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 474 AN: 3472

East Asian (EAS) AF: 0.366 AC: 1888 AN: 5164

South Asian (SAS) AF: 0.114 AC: 550 AN: 4810

European-Finnish (FIN) AF: 0.159 AC: 1677 AN: 10550

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0822 AC: 5587 AN: 67988

Other (OTH) AF: 0.123 AC: 260 AN: 2108

Alfa AF: 0.100 Hom.: 4267

Bravo AF: 0.138

Asia WGS AF: 0.180 AC: 627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.8
DANN	Benign	0.38
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs1916141; hg19: chr2-57514841;