rs6494849

Variant names:

• chr15-70188275-C-A
• rs6494849

Your query was ambiguous. Multiple possible variants found:

• chr15-70188275-C-A
• chr15-70188275-C-T

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 0.209 in 152,068 control chromosomes in the GnomAD database, including 4,265 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 0.21 (4265 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.373 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: 0.209 AC: 31764 AN: 151950 Hom.: 4258 Cov.: 31

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.209 AC: 31791 AN: 152068 Hom.: 4265 Cov.: 31 AF XY: 0.212 AC XY: 15784 AN XY: 74326

African (AFR) AF: 0.378 AC: 15659 AN: 41446

American (AMR) AF: 0.164 AC: 2502 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 383 AN: 3464

East Asian (EAS) AF: 0.183 AC: 947 AN: 5180

South Asian (SAS) AF: 0.257 AC: 1239 AN: 4826

European-Finnish (FIN) AF: 0.186 AC: 1969 AN: 10582

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8514 AN: 67990

Other (OTH) AF: 0.174 AC: 368 AN: 2112

Alfa AF: 0.167 Hom.: 2046

Bravo AF: 0.212

Asia WGS AF: 0.258 AC: 898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.95
DANN	Benign	0.81
PhyloP100		-0.083

Splicing

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

Other links and lift over

dbSNP: rs6494849; hg19: chr15-70480614;