rs691077

Positions:

• chr1-158222163-T-C

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 0.627 in 150,246 control chromosomes in the GnomAD database, including 32,815 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 0.63 (32815 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.628 AC: 94249 AN: 150134 Hom.: 32814 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.872

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.756

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.761

Gnomad MID AF: 0.726

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.627 AC: 94263 AN: 150246 Hom.: 32815 Cov.: 32 AF XY: 0.624 AC XY: 45798 AN XY: 73428

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.681

Gnomad4 ASJ AF: 0.756

Gnomad4 EAS AF: 0.509

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.761

Gnomad4 NFE AF: 0.795

Gnomad4 OTH AF: 0.684

Alfa AF: 0.699 Hom.: 4811

Bravo AF: 0.608

Asia WGS AF: 0.560 AC: 1930 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.0
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs691077; hg19: chr1-158191953;