rs17615220

Variant names:

• chr6-32709636-A-G
• rs17615220

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 0.0562 in 151,952 control chromosomes in the GnomAD database, including 417 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 0.056 (417 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0670
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.079 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: 0.0562 AC: 8537 AN: 151834 Hom.: 416 Cov.: 31

Gnomad AFR AF: 0.0101

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.0579

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0587

Gnomad SAS AF: 0.0824

Gnomad FIN AF: 0.0337

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0808

Gnomad OTH AF: 0.0690

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

GnomAD4 genome AF: 0.0562 AC: 8533 AN: 151952 Hom.: 417 Cov.: 31 AF XY: 0.0548 AC XY: 4068 AN XY: 74290

African (AFR) AF: 0.0101 AC: 418 AN: 41454

American (AMR) AF: 0.0578 AC: 882 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 414 AN: 3468

East Asian (EAS) AF: 0.0585 AC: 302 AN: 5164

South Asian (SAS) AF: 0.0808 AC: 388 AN: 4804

European-Finnish (FIN) AF: 0.0337 AC: 356 AN: 10574

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.0808 AC: 5487 AN: 67922

Other (OTH) AF: 0.0721 AC: 152 AN: 2108

Alfa AF: 0.0725 Hom.: 73

Bravo AF: 0.0550

Asia WGS AF: 0.111 AC: 384 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	11
DANN	Benign	0.59
PhyloP100		0.067

Splicing

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

Other links and lift over

dbSNP: rs17615220; hg19: chr6-32677413;