4-136678862-C-A

Variant names:

• chr4-136678862-C-A
• rs2897305

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 0.241 in 151,512 control chromosomes in the GnomAD database, including 4,458 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 0.24 (4458 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36424 AN: 151398 Hom.: 4456 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.241 AC: 36455 AN: 151512 Hom.: 4458 Cov.: 32 AF XY: 0.240 AC XY: 17796 AN XY: 74022

African (AFR) AF: 0.206 AC: 8519 AN: 41344

American (AMR) AF: 0.221 AC: 3355 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 650 AN: 3462

East Asian (EAS) AF: 0.272 AC: 1398 AN: 5132

South Asian (SAS) AF: 0.210 AC: 1012 AN: 4808

European-Finnish (FIN) AF: 0.273 AC: 2874 AN: 10524

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

European-Non Finnish (NFE) AF: 0.266 AC: 17997 AN: 67770

Other (OTH) AF: 0.230 AC: 481 AN: 2094

Alfa AF: 0.255 Hom.: 2576

Bravo AF: 0.234

Asia WGS AF: 0.239 AC: 831 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.55
DANN	Benign	0.13
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs2897305; hg19: chr4-137600017;