rs1332666

chr1-197015549-A-Gchr1-197015549-A-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 0.384 in 151,736 control chromosomes in the GnomAD database, including 12,795 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 0.38 (12795 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.507 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: 0.384 AC: 58190 AN: 151620 Hom.: 12786 Cov.: 31

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.384 AC: 58212 AN: 151736 Hom.: 12795 Cov.: 31 AF XY: 0.378 AC XY: 28003 AN XY: 74140

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.377

Gnomad4 FIN AF: 0.456

Gnomad4 NFE AF: 0.511

Gnomad4 OTH AF: 0.390

Alfa AF: 0.509 Hom.: 20257

Bravo AF: 0.366

Asia WGS AF: 0.256 AC: 893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	9.0
Dann	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1332666; hg19: chr1-196984679; COSMIC: COSV60014215;