6-85405048-A-G

Position:

• chr6-85405048-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.182 in 152,030 control chromosomes in the GnomAD database, including 3,497 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 0.18 (3497 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27655 AN: 151912 Hom.: 3489 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.0564

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.182 AC: 27697 AN: 152030 Hom.: 3497 Cov.: 32 AF XY: 0.179 AC XY: 13302 AN XY: 74342

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.0565

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.162

Alfa AF: 0.129 Hom.: 1449

Bravo AF: 0.188

Asia WGS AF: 0.126 AC: 438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.1
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9450270; hg19: chr6-86114766;