rs4411692

Variant names:

• chr2-16956438-G-A
• rs4411692

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 0.143 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
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0985 AC: 4080 AN: 41424

American (AMR) AF: 0.136 AC: 2073 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 510 AN: 3470

East Asian (EAS) AF: 0.0112 AC: 58 AN: 5168

South Asian (SAS) AF: 0.117 AC: 563 AN: 4804

European-Finnish (FIN) AF: 0.150 AC: 1568 AN: 10478

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12548 AN: 67948

Other (OTH) AF: 0.135 AC: 285 AN: 2110

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
PhyloP100		0.090

Splicing

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

Other links and lift over

dbSNP: rs4411692; hg19: chr2-17137705;