rs2406041

Variant names:

• chr4-136669703-G-A
• rs2406041

Your query was ambiguous. Multiple possible variants found:

• chr4-136669703-G-A
• chr4-136669703-G-C
• chr4-136669703-G-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 0.202 in 152,080 control chromosomes in the GnomAD database, including 3,564 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 0.20 (3564 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.262 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: 0.202 AC: 30757 AN: 151964 Hom.: 3563 Cov.: 32

Gnomad AFR AF: 0.0941

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.202 AC: 30755 AN: 152080 Hom.: 3564 Cov.: 32 AF XY: 0.202 AC XY: 15000 AN XY: 74342

Gnomad4 AFR AF: 0.0939

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.192

Alfa AF: 0.244 Hom.: 9833

Bravo AF: 0.191

Asia WGS AF: 0.176 AC: 613 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.8
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2406041; hg19: chr4-137590858;