rs2275073

chr1-156061029-C-Achr1-156061029-C-Gchr1-156061029-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 0.615 in 173,600 control chromosomes in the GnomAD database, including 37,947 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 0.60 (32068 hom., cov: 31)
  • Exomes 𝑓: 0.71 (5879 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.373

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.778 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: 0.603 AC: 91531 AN: 151892 Hom.: 32070 Cov.: 31

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.898

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.743

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.784

Gnomad OTH AF: 0.654

GnomAD4 exome AF: 0.707 AC: 15262 AN: 21588 Hom.: 5879 AF XY: 0.703 AC XY: 8081 AN XY: 11488

Gnomad4 AFR exome AF: 0.259

Gnomad4 AMR exome AF: 0.735

Gnomad4 ASJ exome AF: 0.740

Gnomad4 EAS exome AF: 0.172

Gnomad4 SAS exome AF: 0.633

Gnomad4 FIN exome AF: 0.736

Gnomad4 NFE exome AF: 0.781

Gnomad4 OTH exome AF: 0.726

GnomAD4 genome AF: 0.602 AC: 91522 AN: 152012 Hom.: 32068 Cov.: 31 AF XY: 0.601 AC XY: 44651 AN XY: 74324

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.705

Gnomad4 ASJ AF: 0.743

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.613

Gnomad4 FIN AF: 0.755

Gnomad4 NFE AF: 0.784

Gnomad4 OTH AF: 0.652

Alfa AF: 0.714 Hom.: 13463

Bravo AF: 0.584

Asia WGS AF: 0.398 AC: 1386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	0.52
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2275073; hg19: chr1-156030820;