17-32139100-A-C

Variant names:

• chr17-32139100-A-C
• rs9915569

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 0.28 in 151,968 control chromosomes in the GnomAD database, including 7,990 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 0.28 (7990 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.53 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: 0.280 AC: 42460 AN: 151850 Hom.: 7941 Cov.: 31

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.280 AC: 42563 AN: 151968 Hom.: 7990 Cov.: 31 AF XY: 0.276 AC XY: 20522 AN XY: 74268

African (AFR) AF: 0.536 AC: 22184 AN: 41422

American (AMR) AF: 0.222 AC: 3389 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 754 AN: 3466

East Asian (EAS) AF: 0.221 AC: 1142 AN: 5156

South Asian (SAS) AF: 0.260 AC: 1248 AN: 4808

European-Finnish (FIN) AF: 0.137 AC: 1448 AN: 10570

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.172 AC: 11679 AN: 67978

Other (OTH) AF: 0.254 AC: 536 AN: 2112

Alfa AF: 0.253 Hom.: 1028

Bravo AF: 0.295

Asia WGS AF: 0.296 AC: 1029 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.2
DANN	Benign	0.46
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs9915569; hg19: chr17-30466119;