1-8162022-C-T

Variant names:

• chr1-8162022-C-T
• rs4908741

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 0.783 in 152,062 control chromosomes in the GnomAD database, including 47,185 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 0.78 (47185 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.840

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.911 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: 0.782 AC: 118891 AN: 151942 Hom.: 47122 Cov.: 30

Gnomad AFR AF: 0.918

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.719

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.792

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

GnomAD4 genome AF: 0.783 AC: 119012 AN: 152062 Hom.: 47185 Cov.: 30 AF XY: 0.783 AC XY: 58148 AN XY: 74298

Gnomad4 AFR AF: 0.918

Gnomad4 AMR AF: 0.824

Gnomad4 ASJ AF: 0.783

Gnomad4 EAS AF: 0.803

Gnomad4 SAS AF: 0.720

Gnomad4 FIN AF: 0.697

Gnomad4 NFE AF: 0.708

Gnomad4 OTH AF: 0.791

Alfa AF: 0.763 Hom.: 6330

Bravo AF: 0.800

Asia WGS AF: 0.757 AC: 2630 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	0.20
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4908741; hg19: chr1-8222082;