rs10944443

Variant names:

• chr6-89321271-G-C
• rs10944443

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.191 AC: 7929 AN: 41448

American (AMR) AF: 0.188 AC: 2871 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 655 AN: 3468

East Asian (EAS) AF: 0.190 AC: 985 AN: 5176

South Asian (SAS) AF: 0.232 AC: 1118 AN: 4826

European-Finnish (FIN) AF: 0.143 AC: 1511 AN: 10602

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10405 AN: 67970

Other (OTH) AF: 0.181 AC: 381 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.4
DANN	Benign	0.47
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs10944443; hg19: chr6-90030990;