chr6-36239821-A-G

Variant names:

• chr6-36239821-A-G
• rs9380559

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 0.479 in 151,960 control chromosomes in the GnomAD database, including 18,578 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 0.48 (18578 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.721 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: 0.479 AC: 72700 AN: 151842 Hom.: 18523 Cov.: 31

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.479 AC: 72798 AN: 151960 Hom.: 18578 Cov.: 31 AF XY: 0.481 AC XY: 35706 AN XY: 74264

African (AFR) AF: 0.633 AC: 26204 AN: 41426

American (AMR) AF: 0.461 AC: 7038 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1722 AN: 3470

East Asian (EAS) AF: 0.741 AC: 3817 AN: 5152

South Asian (SAS) AF: 0.321 AC: 1540 AN: 4804

European-Finnish (FIN) AF: 0.469 AC: 4956 AN: 10560

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 25994 AN: 67960

Other (OTH) AF: 0.482 AC: 1018 AN: 2110

Alfa AF: 0.423 Hom.: 18751

Bravo AF: 0.495

Asia WGS AF: 0.494 AC: 1717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.67
DANN	Benign	0.52
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs9380559; hg19: chr6-36207598;