chr5-36438152-C-T

Variant names:

• chr5-36438152-C-T
• rs10512653
• ENST00000765258.1:n.133-5088C>T

Variant summary

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

The ENST00000765258.1(ENSG00000299633):​n.133-5088C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,106 control chromosomes in the GnomAD database, including 1,031 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 0.11 (1031 hom., cov: 32)
• Consequence: ENSG00000299633 ENST00000765258.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511
• Publications: 4 publications found

Genes affected

ENSG00000299633 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.14 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
ENSG00000299633	ENST00000765258.1	n.133-5088C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16206 AN: 151988 Hom.: 1031 Cov.: 32

Gnomad AFR AF: 0.0440

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.0681

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.107 AC: 16207 AN: 152106 Hom.: 1031 Cov.: 32 AF XY: 0.104 AC XY: 7768 AN XY: 74352

African (AFR) AF: 0.0440 AC: 1825 AN: 41500

American (AMR) AF: 0.103 AC: 1578 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 727 AN: 3470

East Asian (EAS) AF: 0.0680 AC: 351 AN: 5158

South Asian (SAS) AF: 0.111 AC: 537 AN: 4818

European-Finnish (FIN) AF: 0.101 AC: 1070 AN: 10566

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9690 AN: 67994

Other (OTH) AF: 0.117 AC: 247 AN: 2114

Alfa AF: 0.136 Hom.: 2844

Bravo AF: 0.104

Asia WGS AF: 0.0880 AC: 307 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	0.37
DANN	Benign	0.55
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs10512653; hg19: chr5-36438254;