4-81009660-C-T

Position:

• chr4-81009660-C-T

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 0.816 in 152,260 control chromosomes in the GnomAD database, including 51,899 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 0.82 (51899 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921

ACMG classification

Verdict is Benign. Variant got -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 = 0.918 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.816 AC: 124222 AN: 152142 Hom.: 51870 Cov.: 34

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.866

Gnomad AMR AF: 0.875

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.940

Gnomad SAS AF: 0.870

Gnomad FIN AF: 0.918

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.893

Gnomad OTH AF: 0.816

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

GnomAD4 genome AF: 0.816 AC: 124297 AN: 152260 Hom.: 51899 Cov.: 34 AF XY: 0.820 AC XY: 61077 AN XY: 74452

Gnomad4 AFR AF: 0.628

Gnomad4 AMR AF: 0.875

Gnomad4 ASJ AF: 0.719

Gnomad4 EAS AF: 0.940

Gnomad4 SAS AF: 0.870

Gnomad4 FIN AF: 0.918

Gnomad4 NFE AF: 0.893

Gnomad4 OTH AF: 0.818

Alfa AF: 0.858 Hom.: 9584

Bravo AF: 0.804

Asia WGS AF: 0.886 AC: 3081 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	0.27
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1960445; hg19: chr4-81930814;