rs655167

chr1-187933850-A-Gchr1-187933850-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 0.81 in 152,104 control chromosomes in the GnomAD database, including 51,089 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 0.81 (51089 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.810 AC: 123080 AN: 151988 Hom.: 51063 Cov.: 32

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.885

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.909

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.876

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.810 AC: 123148 AN: 152104 Hom.: 51089 Cov.: 32 AF XY: 0.816 AC XY: 60673 AN XY: 74370

Gnomad4 AFR AF: 0.615

Gnomad4 AMR AF: 0.858

Gnomad4 ASJ AF: 0.853

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.919

Gnomad4 FIN AF: 0.909

Gnomad4 NFE AF: 0.876

Gnomad4 OTH AF: 0.817

Alfa AF: 0.865 Hom.: 105890

Bravo AF: 0.797

Asia WGS AF: 0.938 AC: 3256 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	3.3
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs655167; hg19: chr1-187902981;