rs339321

Variant names:

• chr6-116871027-G-A
• rs339321

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 0.264 in 151,868 control chromosomes in the GnomAD database, including 5,496 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 (5496 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.418 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: 0.264 AC: 40003 AN: 151748 Hom.: 5489 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.264 AC: 40043 AN: 151868 Hom.: 5496 Cov.: 32 AF XY: 0.269 AC XY: 19947 AN XY: 74242

African (AFR) AF: 0.231 AC: 9584 AN: 41408

American (AMR) AF: 0.254 AC: 3874 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 374 AN: 3466

East Asian (EAS) AF: 0.433 AC: 2235 AN: 5162

South Asian (SAS) AF: 0.359 AC: 1725 AN: 4810

European-Finnish (FIN) AF: 0.308 AC: 3239 AN: 10516

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.269 AC: 18300 AN: 67922

Other (OTH) AF: 0.230 AC: 486 AN: 2110

Alfa AF: 0.265 Hom.: 2624

Bravo AF: 0.256

Asia WGS AF: 0.397 AC: 1378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.49
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs339321; hg19: chr6-117192190;