rs6920846

Positions:

• chr6-138128932-A-G
• chr6-138128932-A-T

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 0.336 in 151,914 control chromosomes in the GnomAD database, including 9,281 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 0.34 (9281 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.709 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: 0.336 AC: 50984 AN: 151798 Hom.: 9253 Cov.: 31

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.336 AC: 51052 AN: 151914 Hom.: 9281 Cov.: 31 AF XY: 0.338 AC XY: 25084 AN XY: 74234

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.728

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.345

Alfa AF: 0.346 Hom.: 17013

Bravo AF: 0.339

Asia WGS AF: 0.567 AC: 1970 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.6
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6920846; hg19: chr6-138450069;