rs10947055

Variant names:

• chr6-30125587-T-C
• rs10947055

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 0.106 in 152,252 control chromosomes in the GnomAD database, including 1,219 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 0.11 (1219 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.643

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 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: 0.106 AC: 16138 AN: 152134 Hom.: 1217 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0710

Gnomad ASJ AF: 0.0559

Gnomad EAS AF: 0.00693

Gnomad SAS AF: 0.0759

Gnomad FIN AF: 0.0619

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0774

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.106 AC: 16163 AN: 152252 Hom.: 1219 Cov.: 32 AF XY: 0.103 AC XY: 7683 AN XY: 74460

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.0709

Gnomad4 ASJ AF: 0.0559

Gnomad4 EAS AF: 0.00713

Gnomad4 SAS AF: 0.0764

Gnomad4 FIN AF: 0.0619

Gnomad4 NFE AF: 0.0774

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0859 Hom.: 448

Bravo AF: 0.111

Asia WGS AF: 0.0460 AC: 161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10947055; hg19: chr6-30093364;