6-36670859-G-A

Variant names:

• chr6-36670859-G-A
• rs1321309

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 0.382 in 152,070 control chromosomes in the GnomAD database, including 12,572 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 0.38 (12572 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.498
• Publications: 25 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.484 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: 0.382 AC: 58069 AN: 151950 Hom.: 12577 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.382 AC: 58054 AN: 152070 Hom.: 12572 Cov.: 32 AF XY: 0.382 AC XY: 28393 AN XY: 74328

African (AFR) AF: 0.182 AC: 7562 AN: 41496

American (AMR) AF: 0.334 AC: 5113 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1299 AN: 3464

East Asian (EAS) AF: 0.301 AC: 1559 AN: 5172

South Asian (SAS) AF: 0.491 AC: 2361 AN: 4808

European-Finnish (FIN) AF: 0.528 AC: 5580 AN: 10562

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33163 AN: 67964

Other (OTH) AF: 0.348 AC: 735 AN: 2110

Alfa AF: 0.437 Hom.: 15374

Bravo AF: 0.354

Asia WGS AF: 0.381 AC: 1325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	13
DANN	Benign	0.87
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs1321309; hg19: chr6-36638636;