rs6494167

Variant names:

• chr15-60143148-T-C
• rs6494167

Your query was ambiguous. Multiple possible variants found:

• chr15-60143148-T-C
• chr15-60143148-T-G

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 0.478 in 151,916 control chromosomes in the GnomAD database, including 17,646 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 0.48 (17646 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.502
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.668 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: 0.478 AC: 72524 AN: 151796 Hom.: 17626 Cov.: 32

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.478 AC: 72587 AN: 151916 Hom.: 17646 Cov.: 32 AF XY: 0.482 AC XY: 35817 AN XY: 74268

African (AFR) AF: 0.423 AC: 17543 AN: 41438

American (AMR) AF: 0.486 AC: 7408 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1537 AN: 3464

East Asian (EAS) AF: 0.687 AC: 3556 AN: 5174

South Asian (SAS) AF: 0.527 AC: 2540 AN: 4820

European-Finnish (FIN) AF: 0.529 AC: 5594 AN: 10584

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32840 AN: 67866

Other (OTH) AF: 0.466 AC: 982 AN: 2108

Alfa AF: 0.470 Hom.: 28509

Bravo AF: 0.473

Asia WGS AF: 0.596 AC: 2072 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.8
DANN	Benign	0.75
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs6494167; hg19: chr15-60435347;