rs10503993

Variant names:

• chr8-36697515-G-A
• rs10503993
• ENST00000524132.6:n.529+4306C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000524132.6(ENSG00000253363):​n.529+4306C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,118 control chromosomes in the GnomAD database, including 3,356 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 (3356 hom., cov: 32)
• Consequence: ENSG00000253363 ENST00000524132.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.714
• Publications: 0 publications found

Genes affected

ENSG00000253363 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.389 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
ENSG00000253363	ENST00000524132.6	n.529+4306C>T		intron_variant	Intron 4 of 4	4
ENSG00000253363	ENST00000651399.1	n.516+4306C>T		intron_variant	Intron 4 of 5
ENSG00000253363	ENST00000656455.2	n.484+4306C>T		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18971 AN: 152000 Hom.: 3341 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0444

Gnomad ASJ AF: 0.00433

Gnomad EAS AF: 0.0421

Gnomad SAS AF: 0.0727

Gnomad FIN AF: 0.0350

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0124

Gnomad OTH AF: 0.0981

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

GnomAD4 genome AF: 0.125 AC: 19032 AN: 152118 Hom.: 3356 Cov.: 32 AF XY: 0.122 AC XY: 9061 AN XY: 74360

African (AFR) AF: 0.394 AC: 16332 AN: 41456

American (AMR) AF: 0.0443 AC: 677 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00433 AC: 15 AN: 3466

East Asian (EAS) AF: 0.0424 AC: 219 AN: 5170

South Asian (SAS) AF: 0.0723 AC: 349 AN: 4826

European-Finnish (FIN) AF: 0.0350 AC: 371 AN: 10590

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0124 AC: 845 AN: 68004

Other (OTH) AF: 0.0994 AC: 210 AN: 2112

Alfa AF: 0.0773 Hom.: 234

Bravo AF: 0.135

Asia WGS AF: 0.111 AC: 384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.4
DANN	Benign	0.59
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs10503993; hg19: chr8-36555033;