rs6908010

Variant names:

• chr6-12217766-T-G
• rs6908010

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;