1-156882671-A-C

Variant names:

• chr1-156882671-A-C
• rs2768759

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 0.524 in 151,998 control chromosomes in the GnomAD database, including 25,984 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 0.52 (25984 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790
• Publications: 21 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79586 AN: 151878 Hom.: 25984 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.756

Gnomad EAS AF: 0.0546

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.524 AC: 79592 AN: 151998 Hom.: 25984 Cov.: 32 AF XY: 0.518 AC XY: 38453 AN XY: 74284

African (AFR) AF: 0.167 AC: 6913 AN: 41440

American (AMR) AF: 0.556 AC: 8509 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.756 AC: 2625 AN: 3470

East Asian (EAS) AF: 0.0549 AC: 283 AN: 5156

South Asian (SAS) AF: 0.385 AC: 1851 AN: 4806

European-Finnish (FIN) AF: 0.739 AC: 7815 AN: 10576

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.730 AC: 49579 AN: 67938

Other (OTH) AF: 0.551 AC: 1164 AN: 2114

Alfa AF: 0.625 Hom.: 48863

Bravo AF: 0.500

Asia WGS AF: 0.239 AC: 833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	10
DANN	Benign	0.74
PhyloP100		0.079

Splicing

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

Other links and lift over

dbSNP: rs2768759; hg19: chr1-156852463;