1-17918213-C-T

Variant names:

• chr1-17918213-C-T
• rs6686929

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 0.531 in 151,964 control chromosomes in the GnomAD database, including 21,964 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 0.53 (21964 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.301
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80627 AN: 151844 Hom.: 21957 Cov.: 32

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.531 AC: 80679 AN: 151964 Hom.: 21964 Cov.: 32 AF XY: 0.536 AC XY: 39815 AN XY: 74278

African (AFR) AF: 0.427 AC: 17712 AN: 41446

American (AMR) AF: 0.484 AC: 7399 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1606 AN: 3472

East Asian (EAS) AF: 0.676 AC: 3466 AN: 5124

South Asian (SAS) AF: 0.557 AC: 2678 AN: 4808

European-Finnish (FIN) AF: 0.691 AC: 7309 AN: 10574

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.572 AC: 38869 AN: 67954

Other (OTH) AF: 0.516 AC: 1087 AN: 2108

Alfa AF: 0.546 Hom.: 60392

Bravo AF: 0.508

Asia WGS AF: 0.593 AC: 2063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.2
DANN	Benign	0.54
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs6686929; hg19: chr1-18244707; COSMIC: COSV59928494;