rs4411692

Positions:

• chr2-16956438-G-A

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 0.143 in 151,844 control chromosomes in the GnomAD database, including 1,708 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 (1708 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.182 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: 0.143 AC: 21763 AN: 151724 Hom.: 1708 Cov.: 32

Gnomad AFR AF: 0.0987

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0112

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.143 AC: 21766 AN: 151844 Hom.: 1708 Cov.: 32 AF XY: 0.140 AC XY: 10360 AN XY: 74178

Gnomad4 AFR AF: 0.0985

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.0112

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.135

Alfa AF: 0.156 Hom.: 288

Bravo AF: 0.138

Asia WGS AF: 0.0780 AC: 273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.6
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4411692; hg19: chr2-17137705;