rs6908010

Positions:

• chr6-12217766-T-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 0.558 in 151,984 control chromosomes in the GnomAD database, including 23,675 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 0.56 (23675 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84693 AN: 151864 Hom.: 23658 Cov.: 32

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.558 AC: 84763 AN: 151984 Hom.: 23675 Cov.: 32 AF XY: 0.557 AC XY: 41384 AN XY: 74258

Gnomad4 AFR AF: 0.592

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.543

Gnomad4 SAS AF: 0.541

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.554

Gnomad4 OTH AF: 0.606

Alfa AF: 0.561 Hom.: 30997

Bravo AF: 0.556

Asia WGS AF: 0.567 AC: 1973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.1
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6908010; hg19: chr6-12217999;