rs17216035

Variant names:

• chr3-6439938-C-A
• rs17216035

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.265 in 151,958 control chromosomes in the GnomAD database, including 5,648 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 (5648 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.676

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.339 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: 0.265 AC: 40230 AN: 151840 Hom.: 5638 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.201

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.265 AC: 40256 AN: 151958 Hom.: 5648 Cov.: 32 AF XY: 0.266 AC XY: 19753 AN XY: 74252

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.272

Alfa AF: 0.285 Hom.: 10705

Bravo AF: 0.261

Asia WGS AF: 0.287 AC: 993 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.22
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17216035; hg19: chr3-6481625;