4-178431951-T-C

Variant names:

• chr4-178431951-T-C
• rs2706011

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 0.892 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.892 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

Gnomad4 AFR AF: 0.897

Gnomad4 AMR AF: 0.909

Gnomad4 ASJ AF: 0.882

Gnomad4 EAS AF: 0.874

Gnomad4 SAS AF: 0.903

Gnomad4 FIN AF: 0.912

Gnomad4 NFE AF: 0.884

Gnomad4 OTH AF: 0.879

Alfa AF: 0.893 Hom.: 13459

Bravo AF: 0.892

Asia WGS AF: 0.862 AC: 2998 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2706011; hg19: chr4-179353105;