rs4971342

Positions:

• chr2-941001-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.171 in 152,156 control chromosomes in the GnomAD database, including 2,661 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 0.17 (2661 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26026 AN: 152038 Hom.: 2660 Cov.: 32

Gnomad AFR AF: 0.0927

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.0301

Gnomad SAS AF: 0.0947

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.171 AC: 26038 AN: 152156 Hom.: 2661 Cov.: 32 AF XY: 0.168 AC XY: 12497 AN XY: 74394

Gnomad4 AFR AF: 0.0928

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.0300

Gnomad4 SAS AF: 0.0940

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.168

Alfa AF: 0.204 Hom.: 2009

Bravo AF: 0.160

Asia WGS AF: 0.0920 AC: 320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.16
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4971342; hg19: chr2-936687;