rs10943944

Variant names:

• chr6-83502217-C-T
• rs10943944

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 0.24 in 151,918 control chromosomes in the GnomAD database, including 5,382 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 0.24 (5382 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.752

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 = 0.418 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: 0.239 AC: 36344 AN: 151798 Hom.: 5373 Cov.: 31

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.240 AC: 36400 AN: 151918 Hom.: 5382 Cov.: 31 AF XY: 0.234 AC XY: 17387 AN XY: 74252

Gnomad4 AFR AF: 0.423

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.214

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.244

Alfa AF: 0.178 Hom.: 3986

Bravo AF: 0.253

Asia WGS AF: 0.202 AC: 701 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10943944; hg19: chr6-84211936;