rs10944443

chr6-89321271-G-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;