chr6-94056539-G-A

Variant names:

• chr6-94056539-G-A
• rs4302647

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 0.0914 in 151,826 control chromosomes in the GnomAD database, including 1,547 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 0.091 (1547 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.448
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.265 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: 0.0914 AC: 13861 AN: 151708 Hom.: 1546 Cov.: 32

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0372

Gnomad ASJ AF: 0.0804

Gnomad EAS AF: 0.0450

Gnomad SAS AF: 0.0956

Gnomad FIN AF: 0.00567

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0144

Gnomad OTH AF: 0.0761

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

GnomAD4 genome AF: 0.0914 AC: 13882 AN: 151826 Hom.: 1547 Cov.: 32 AF XY: 0.0915 AC XY: 6789 AN XY: 74214

African (AFR) AF: 0.269 AC: 11132 AN: 41398

American (AMR) AF: 0.0371 AC: 564 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.0804 AC: 279 AN: 3468

East Asian (EAS) AF: 0.0453 AC: 234 AN: 5162

South Asian (SAS) AF: 0.0944 AC: 454 AN: 4808

European-Finnish (FIN) AF: 0.00567 AC: 60 AN: 10578

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0144 AC: 978 AN: 67882

Other (OTH) AF: 0.0754 AC: 159 AN: 2110

Alfa AF: 0.0309 Hom.: 63

Bravo AF: 0.0991

Asia WGS AF: 0.0700 AC: 245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.56
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs4302647; hg19: chr6-94766257;