4-178431951-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;