6-132566206-A-G

Variant names:

• chr6-132566206-A-G
• rs4085406

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 0.458 in 151,954 control chromosomes in the GnomAD database, including 16,584 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 0.46 (16584 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.434
• Publications: 3 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 = 0.831 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: 0.458 AC: 69581 AN: 151836 Hom.: 16574 Cov.: 32

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.853

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.458 AC: 69622 AN: 151954 Hom.: 16584 Cov.: 32 AF XY: 0.461 AC XY: 34241 AN XY: 74272

African (AFR) AF: 0.435 AC: 18023 AN: 41436

American (AMR) AF: 0.408 AC: 6239 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1624 AN: 3466

East Asian (EAS) AF: 0.852 AC: 4407 AN: 5170

South Asian (SAS) AF: 0.550 AC: 2651 AN: 4818

European-Finnish (FIN) AF: 0.399 AC: 4201 AN: 10528

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.456 AC: 30982 AN: 67946

Other (OTH) AF: 0.474 AC: 1003 AN: 2114

Alfa AF: 0.449 Hom.: 5617

Bravo AF: 0.459

Asia WGS AF: 0.700 AC: 2431 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.53
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs4085406; hg19: chr6-132887345;