5-56441810-C-T

Variant names:

• chr5-56441810-C-T
• rs158210

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 0.0915 in 152,042 control chromosomes in the GnomAD database, including 699 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 0.092 (699 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.235 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: 0.0916 AC: 13921 AN: 151924 Hom.: 701 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0640

Gnomad ASJ AF: 0.0914

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0763

Gnomad OTH AF: 0.0877

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

GnomAD4 genome AF: 0.0915 AC: 13912 AN: 152042 Hom.: 699 Cov.: 32 AF XY: 0.0938 AC XY: 6967 AN XY: 74288

African (AFR) AF: 0.102 AC: 4227 AN: 41454

American (AMR) AF: 0.0637 AC: 974 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0914 AC: 317 AN: 3468

East Asian (EAS) AF: 0.246 AC: 1272 AN: 5168

South Asian (SAS) AF: 0.131 AC: 632 AN: 4812

European-Finnish (FIN) AF: 0.105 AC: 1104 AN: 10556

Middle Eastern (MID) AF: 0.0479 AC: 14 AN: 292

European-Non Finnish (NFE) AF: 0.0763 AC: 5188 AN: 67986

Other (OTH) AF: 0.0868 AC: 183 AN: 2108

Alfa AF: 0.0809 Hom.: 1437

Bravo AF: 0.0895

Asia WGS AF: 0.166 AC: 578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.3
DANN	Benign	0.50
PhyloP100		-0.085

Splicing

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

Other links and lift over

dbSNP: rs158210; hg19: chr5-55737637;