rs2406041

Positions:

• chr4-136669703-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 0.202 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;