rs10512623

Variant names:

• chr5-35585285-C-T
• rs10512623

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 0.121 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
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• 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

African (AFR) AF: 0.0399 AC: 1652 AN: 41444

American (AMR) AF: 0.121 AC: 1833 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 592 AN: 3460

East Asian (EAS) AF: 0.132 AC: 682 AN: 5152

South Asian (SAS) AF: 0.190 AC: 913 AN: 4804

European-Finnish (FIN) AF: 0.206 AC: 2169 AN: 10518

Middle Eastern (MID) AF: 0.164 AC: 48 AN: 292

European-Non Finnish (NFE) AF: 0.150 AC: 10203 AN: 67842

Other (OTH) AF: 0.123 AC: 260 AN: 2106

Alfa AF: 0.136 Hom.: 3673

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
PhyloP100		-0.0090

Splicing

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

Other links and lift over

dbSNP: rs10512623; hg19: chr5-35585387;