4-136007297-C-T

Variant names:

• chr4-136007297-C-T
• rs9990901

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 0.871 in 152,106 control chromosomes in the GnomAD database, including 57,727 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 0.87 (57727 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.933 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: 0.871 AC: 132343 AN: 151988 Hom.: 57685 Cov.: 33

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.878

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.955

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.890

Gnomad OTH AF: 0.879

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

GnomAD4 genome AF: 0.871 AC: 132443 AN: 152106 Hom.: 57727 Cov.: 33 AF XY: 0.870 AC XY: 64664 AN XY: 74364

African (AFR) AF: 0.831 AC: 34495 AN: 41502

American (AMR) AF: 0.879 AC: 13436 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.846 AC: 2938 AN: 3472

East Asian (EAS) AF: 0.955 AC: 4938 AN: 5168

South Asian (SAS) AF: 0.861 AC: 4158 AN: 4830

European-Finnish (FIN) AF: 0.866 AC: 9174 AN: 10588

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.890 AC: 60439 AN: 67944

Other (OTH) AF: 0.880 AC: 1854 AN: 2108

Alfa AF: 0.859 Hom.: 21175

Bravo AF: 0.869

Asia WGS AF: 0.889 AC: 3083 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.68
DANN	Benign	0.15
PhyloP100		0.025

Splicing

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

Other links and lift over

dbSNP: rs9990901; hg19: chr4-136928452;