chr6-20365831-G-A

Variant names:

• chr6-20365831-G-A
• rs9366347

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 0.293 in 151,892 control chromosomes in the GnomAD database, including 6,693 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 0.29 (6693 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.446 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: 0.293 AC: 44414 AN: 151774 Hom.: 6677 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.293 AC: 44467 AN: 151892 Hom.: 6693 Cov.: 32 AF XY: 0.299 AC XY: 22162 AN XY: 74218

African (AFR) AF: 0.306 AC: 12664 AN: 41398

American (AMR) AF: 0.327 AC: 4988 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 898 AN: 3466

East Asian (EAS) AF: 0.461 AC: 2384 AN: 5166

South Asian (SAS) AF: 0.375 AC: 1804 AN: 4816

European-Finnish (FIN) AF: 0.285 AC: 3000 AN: 10522

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17757 AN: 67956

Other (OTH) AF: 0.273 AC: 575 AN: 2104

Alfa AF: 0.279 Hom.: 10336

Bravo AF: 0.296

Asia WGS AF: 0.401 AC: 1395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.8
DANN	Benign	0.75
PhyloP100		-0.077

Splicing

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

Other links and lift over

dbSNP: rs9366347; hg19: chr6-20366062;