rs4356177

Variant names:

• chr10-44668120-T-C
• rs4356177

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 0.13 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.131 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

Gnomad4 AFR AF: 0.0853

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.000967

Gnomad4 SAS AF: 0.0511

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.125

Alfa AF: 0.156 Hom.: 937

Bravo AF: 0.129

Asia WGS AF: 0.0370 AC: 128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4356177; hg19: chr10-45163568;