rs6496669

Variant names:

• chr15-90352033-G-A
• rs6496669

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 0.229 in 152,178 control chromosomes in the GnomAD database, including 4,350 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 0.23 (4350 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.323 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: 0.229 AC: 34855 AN: 152060 Hom.: 4341 Cov.: 33

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.229 AC: 34884 AN: 152178 Hom.: 4350 Cov.: 33 AF XY: 0.228 AC XY: 16950 AN XY: 74400

African (AFR) AF: 0.328 AC: 13593 AN: 41498

American (AMR) AF: 0.148 AC: 2271 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 696 AN: 3472

East Asian (EAS) AF: 0.231 AC: 1195 AN: 5162

South Asian (SAS) AF: 0.237 AC: 1146 AN: 4828

European-Finnish (FIN) AF: 0.175 AC: 1851 AN: 10606

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13407 AN: 67990

Other (OTH) AF: 0.220 AC: 466 AN: 2114

Alfa AF: 0.207 Hom.: 9866

Bravo AF: 0.229

Asia WGS AF: 0.250 AC: 870 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.1
DANN	Benign	0.70
PhyloP100		0.0050
PromoterAI		0.017	Neutral

Splicing

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

Other links and lift over

dbSNP: rs6496669; hg19: chr15-90895265;