1-17918213-C-T

Variant names:

• chr1-17918213-C-T
• rs6686929

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 0.531 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.557

Gnomad4 FIN AF: 0.691

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.516

Alfa AF: 0.544 Hom.: 22736

Bravo AF: 0.508

Asia WGS AF: 0.593 AC: 2063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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