rs10944443

Variant names:

• chr6-89321271-G-C
• rs10944443

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 0.172 in 152,084 control chromosomes in the GnomAD database, including 2,271 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 0.17 (2271 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.232

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.22 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: 0.172 AC: 26109 AN: 151966 Hom.: 2271 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.172 AC: 26127 AN: 152084 Hom.: 2271 Cov.: 32 AF XY: 0.174 AC XY: 12965 AN XY: 74348

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.181

Alfa AF: 0.156 Hom.: 226

Bravo AF: 0.174

Asia WGS AF: 0.225 AC: 783 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.4
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10944443; hg19: chr6-90030990;