chr1-158222163-T-C

Variant names:

• chr1-158222163-T-C
• rs691077

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.303 AC: 12440 AN: 41000

American (AMR) AF: 0.681 AC: 10276 AN: 15094

Ashkenazi Jewish (ASJ) AF: 0.756 AC: 2602 AN: 3440

East Asian (EAS) AF: 0.509 AC: 2612 AN: 5132

South Asian (SAS) AF: 0.553 AC: 2637 AN: 4766

European-Finnish (FIN) AF: 0.761 AC: 7915 AN: 10400

Middle Eastern (MID) AF: 0.712 AC: 208 AN: 292

European-Non Finnish (NFE) AF: 0.795 AC: 53366 AN: 67146

Other (OTH) AF: 0.684 AC: 1415 AN: 2068

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.0
DANN	Benign	0.27
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs691077; hg19: chr1-158191953;