rs6496667

Variant names:

• chr15-90350436-C-A
• rs6496667

Your query was ambiguous. Multiple possible variants found:

• chr15-90350436-C-A
• chr15-90350436-C-G
• chr15-90350436-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 0.261 in 151,950 control chromosomes in the GnomAD database, including 5,786 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 0.26 (5786 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.393 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: 0.261 AC: 39593 AN: 151832 Hom.: 5774 Cov.: 31

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.261 AC: 39641 AN: 151950 Hom.: 5786 Cov.: 31 AF XY: 0.261 AC XY: 19425 AN XY: 74286

African (AFR) AF: 0.398 AC: 16461 AN: 41380

American (AMR) AF: 0.190 AC: 2895 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 712 AN: 3468

East Asian (EAS) AF: 0.330 AC: 1707 AN: 5172

South Asian (SAS) AF: 0.278 AC: 1340 AN: 4818

European-Finnish (FIN) AF: 0.207 AC: 2188 AN: 10552

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.199 AC: 13550 AN: 67982

Other (OTH) AF: 0.248 AC: 522 AN: 2108

Alfa AF: 0.216 Hom.: 13092

Bravo AF: 0.265

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.9
DANN	Benign	0.55
PhyloP100		0.029

Splicing

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

Other links and lift over

dbSNP: rs6496667; hg19: chr15-90893668;