rs10512623

Variant names:

• chr5-35585285-C-T
• rs10512623

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 0.121 in 151,726 control chromosomes in the GnomAD database, including 1,373 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 0.12 (1373 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.18 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: 0.121 AC: 18401 AN: 151608 Hom.: 1373 Cov.: 31

Gnomad AFR AF: 0.0399

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.121 AC: 18407 AN: 151726 Hom.: 1373 Cov.: 31 AF XY: 0.125 AC XY: 9252 AN XY: 74146

Gnomad4 AFR AF: 0.0399

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.123

Alfa AF: 0.146 Hom.: 3068

Bravo AF: 0.108

Asia WGS AF: 0.161 AC: 560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.1
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512623; hg19: chr5-35585387;