rs927485

Variant names:

• chr6-44570402-G-A
• rs927485

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.597 in 152,100 control chromosomes in the GnomAD database, including 31,833 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 0.60 (31833 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.22
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 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: 0.597 AC: 90736 AN: 151982 Hom.: 31822 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.910

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.597 AC: 90755 AN: 152100 Hom.: 31833 Cov.: 32 AF XY: 0.609 AC XY: 45259 AN XY: 74356

African (AFR) AF: 0.205 AC: 8523 AN: 41492

American (AMR) AF: 0.698 AC: 10661 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.739 AC: 2564 AN: 3470

East Asian (EAS) AF: 0.911 AC: 4706 AN: 5168

South Asian (SAS) AF: 0.797 AC: 3838 AN: 4814

European-Finnish (FIN) AF: 0.812 AC: 8609 AN: 10600

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.735 AC: 49929 AN: 67966

Other (OTH) AF: 0.599 AC: 1266 AN: 2112

Alfa AF: 0.695 Hom.: 98034

Bravo AF: 0.570

Asia WGS AF: 0.803 AC: 2789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	16
DANN	Benign	0.66
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs927485; hg19: chr6-44538139;