6-85407411-A-G

Variant names:

• chr6-85407411-A-G
• rs494562

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 0.161 in 152,050 control chromosomes in the GnomAD database, including 2,703 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 0.16 (2703 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.430
• Publications: 30 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 (AFR) allele frequency at 95% confidence interval = 0.311 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: 0.161 AC: 24404 AN: 151932 Hom.: 2692 Cov.: 31

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.0923

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.0566

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.0971

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.161 AC: 24445 AN: 152050 Hom.: 2703 Cov.: 31 AF XY: 0.159 AC XY: 11846 AN XY: 74328

African (AFR) AF: 0.315 AC: 13068 AN: 41424

American (AMR) AF: 0.111 AC: 1696 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 432 AN: 3472

East Asian (EAS) AF: 0.0567 AC: 293 AN: 5166

South Asian (SAS) AF: 0.131 AC: 630 AN: 4800

European-Finnish (FIN) AF: 0.0971 AC: 1029 AN: 10600

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6857 AN: 67982

Other (OTH) AF: 0.143 AC: 303 AN: 2114

Alfa AF: 0.119 Hom.: 4305

Bravo AF: 0.166

Asia WGS AF: 0.115 AC: 401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.0
DANN	Benign	0.51
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs494562; hg19: chr6-86117129;