1-234534101-T-C

Variant names:

• chr1-234534101-T-C
• rs271762

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.494 in 152,052 control chromosomes in the GnomAD database, including 19,689 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 0.49 (19689 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.24

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.9 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: 0.494 AC: 75078 AN: 151934 Hom.: 19662 Cov.: 32

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.922

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.494 AC: 75157 AN: 152052 Hom.: 19689 Cov.: 32 AF XY: 0.506 AC XY: 37643 AN XY: 74324

Gnomad4 AFR AF: 0.551

Gnomad4 AMR AF: 0.575

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.922

Gnomad4 SAS AF: 0.775

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.495

Alfa AF: 0.420 Hom.: 14152

Bravo AF: 0.505

Asia WGS AF: 0.825 AC: 2864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	17
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs271762; hg19: chr1-234669847;