rs1963273

Variant names:

• chr1-171353307-C-T
• rs1963273

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 0.33 in 152,006 control chromosomes in the GnomAD database, including 8,335 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 0.33 (8335 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.42 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: 0.330 AC: 50167 AN: 151888 Hom.: 8326 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.330 AC: 50206 AN: 152006 Hom.: 8335 Cov.: 32 AF XY: 0.332 AC XY: 24662 AN XY: 74286

Gnomad4 AFR AF: 0.338

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.352

Alfa AF: 0.328 Hom.: 17284

Bravo AF: 0.330

Asia WGS AF: 0.391 AC: 1360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.2
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1963273; hg19: chr1-171322446;