5-89813933-C-T

Variant names:

• chr5-89813933-C-T
• rs10514317

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 0.0866 in 151,746 control chromosomes in the GnomAD database, including 753 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 0.087 (753 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.313
• Publications: 5 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 (NFE) allele frequency at 95% confidence interval = 0.124 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: 0.0867 AC: 13148 AN: 151628 Hom.: 750 Cov.: 32

Gnomad AFR AF: 0.0233

Gnomad AMI AF: 0.0791

Gnomad AMR AF: 0.0890

Gnomad ASJ AF: 0.0551

Gnomad EAS AF: 0.000776

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0350

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0866 AC: 13148 AN: 151746 Hom.: 753 Cov.: 32 AF XY: 0.0849 AC XY: 6293 AN XY: 74154

African (AFR) AF: 0.0233 AC: 964 AN: 41452

American (AMR) AF: 0.0892 AC: 1356 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.0551 AC: 191 AN: 3464

East Asian (EAS) AF: 0.000778 AC: 4 AN: 5142

South Asian (SAS) AF: 0.124 AC: 598 AN: 4808

European-Finnish (FIN) AF: 0.114 AC: 1206 AN: 10544

Middle Eastern (MID) AF: 0.0377 AC: 11 AN: 292

European-Non Finnish (NFE) AF: 0.126 AC: 8537 AN: 67822

Other (OTH) AF: 0.0992 AC: 209 AN: 2106

Alfa AF: 0.104 Hom.: 1331

Bravo AF: 0.0824

Asia WGS AF: 0.0550 AC: 191 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.41
DANN	Benign	0.56
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs10514317; hg19: chr5-89109750;