chr3-6439938-C-A

Variant names:

• chr3-6439938-C-A
• rs17216035

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 0.265 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.181 AC: 7518 AN: 41494

American (AMR) AF: 0.329 AC: 5018 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 826 AN: 3468

East Asian (EAS) AF: 0.352 AC: 1812 AN: 5146

South Asian (SAS) AF: 0.199 AC: 956 AN: 4812

European-Finnish (FIN) AF: 0.338 AC: 3560 AN: 10528

Middle Eastern (MID) AF: 0.192 AC: 56 AN: 292

European-Non Finnish (NFE) AF: 0.290 AC: 19733 AN: 67964

Other (OTH) AF: 0.272 AC: 575 AN: 2112

Alfa AF: 0.283 Hom.: 24342

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
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs17216035; hg19: chr3-6481625;