1-152618666-A-C

Variant names:

• chr1-152618666-A-C
• rs1886734

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 0.58 in 152,066 control chromosomes in the GnomAD database, including 26,256 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 0.58 (26256 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.64 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: 0.580 AC: 88086 AN: 151948 Hom.: 26249 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.580 AC: 88127 AN: 152066 Hom.: 26256 Cov.: 32 AF XY: 0.584 AC XY: 43436 AN XY: 74330

African (AFR) AF: 0.422 AC: 17499 AN: 41468

American (AMR) AF: 0.623 AC: 9518 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2154 AN: 3464

East Asian (EAS) AF: 0.614 AC: 3178 AN: 5172

South Asian (SAS) AF: 0.630 AC: 3039 AN: 4820

European-Finnish (FIN) AF: 0.661 AC: 6989 AN: 10574

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.645 AC: 43821 AN: 67966

Other (OTH) AF: 0.582 AC: 1230 AN: 2112

Alfa AF: 0.611 Hom.: 15315

Bravo AF: 0.567

Asia WGS AF: 0.582 AC: 2025 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.73
DANN	Benign	0.72
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs1886734; hg19: chr1-152591142;