10-44668120-T-C

Variant names:

• chr10-44668120-T-C
• rs4356177

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 0.13 in 152,076 control chromosomes in the GnomAD database, including 1,508 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 0.13 (1508 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.956
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19840 AN: 151956 Hom.: 1508 Cov.: 32

Gnomad AFR AF: 0.0853

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.000966

Gnomad SAS AF: 0.0516

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.130 AC: 19845 AN: 152076 Hom.: 1508 Cov.: 32 AF XY: 0.126 AC XY: 9392 AN XY: 74354

African (AFR) AF: 0.0853 AC: 3540 AN: 41478

American (AMR) AF: 0.116 AC: 1775 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 455 AN: 3466

East Asian (EAS) AF: 0.000967 AC: 5 AN: 5168

South Asian (SAS) AF: 0.0511 AC: 246 AN: 4818

European-Finnish (FIN) AF: 0.132 AC: 1392 AN: 10568

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11922 AN: 67972

Other (OTH) AF: 0.125 AC: 265 AN: 2114

Alfa AF: 0.157 Hom.: 1052

Bravo AF: 0.129

Asia WGS AF: 0.0370 AC: 128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	7.8
DANN	Benign	0.57
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs4356177; hg19: chr10-45163568;