chr4-136669703-G-A

Variant names:

• chr4-136669703-G-A
• rs2406041

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 0.202 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0939 AC: 3898 AN: 41502

American (AMR) AF: 0.204 AC: 3121 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 617 AN: 3470

East Asian (EAS) AF: 0.147 AC: 760 AN: 5164

South Asian (SAS) AF: 0.202 AC: 975 AN: 4826

European-Finnish (FIN) AF: 0.265 AC: 2797 AN: 10574

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 18012 AN: 67960

Other (OTH) AF: 0.192 AC: 405 AN: 2112

Alfa AF: 0.240 Hom.: 20087

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
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs2406041; hg19: chr4-137590858;