1-17508246-C-T

Variant names:

• chr1-17508246-C-T
• rs2254135

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 0.612 in 151,966 control chromosomes in the GnomAD database, including 29,207 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 0.61 (29207 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.513
• Publications: 6 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 (AMR) allele frequency at 95% confidence interval = 0.71 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: 0.612 AC: 92931 AN: 151848 Hom.: 29196 Cov.: 31

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.662

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.612 AC: 92975 AN: 151966 Hom.: 29207 Cov.: 31 AF XY: 0.607 AC XY: 45073 AN XY: 74270

African (AFR) AF: 0.469 AC: 19433 AN: 41420

American (AMR) AF: 0.721 AC: 10998 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.695 AC: 2411 AN: 3470

East Asian (EAS) AF: 0.663 AC: 3427 AN: 5170

South Asian (SAS) AF: 0.594 AC: 2857 AN: 4810

European-Finnish (FIN) AF: 0.554 AC: 5847 AN: 10558

Middle Eastern (MID) AF: 0.644 AC: 188 AN: 292

European-Non Finnish (NFE) AF: 0.675 AC: 45856 AN: 67970

Other (OTH) AF: 0.613 AC: 1294 AN: 2112

Alfa AF: 0.662 Hom.: 94306

Bravo AF: 0.622

Asia WGS AF: 0.610 AC: 2121 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	1.6
DANN	Benign	0.70
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs2254135; hg19: chr1-17834742; COSMIC: COSV59927778;