4-178431951-T-C

Variant names:

• chr4-178431951-T-C
• rs2706011

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 0.892 in 152,204 control chromosomes in the GnomAD database, including 60,565 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 0.89 (60565 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.896 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: 0.892 AC: 135678 AN: 152086 Hom.: 60524 Cov.: 32

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.908

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.912

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.884

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.892 AC: 135775 AN: 152204 Hom.: 60565 Cov.: 32 AF XY: 0.896 AC XY: 66651 AN XY: 74400

African (AFR) AF: 0.897 AC: 37253 AN: 41532

American (AMR) AF: 0.909 AC: 13883 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.882 AC: 3063 AN: 3472

East Asian (EAS) AF: 0.874 AC: 4503 AN: 5152

South Asian (SAS) AF: 0.903 AC: 4362 AN: 4828

European-Finnish (FIN) AF: 0.912 AC: 9675 AN: 10610

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.884 AC: 60155 AN: 68018

Other (OTH) AF: 0.879 AC: 1852 AN: 2108

Alfa AF: 0.894 Hom.: 13786

Bravo AF: 0.892

Asia WGS AF: 0.862 AC: 2998 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.84
DANN	Benign	0.61
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs2706011; hg19: chr4-179353105;