13-108340507-C-T

Variant names:

• chr13-108340507-C-T
• rs7333523
• ENST00000636252.1:n.125+4935C>T

Variant summary

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

The ENST00000636252.1(ENSG00000283384):​n.125+4935C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 151,998 control chromosomes in the GnomAD database, including 3,505 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 0.20 (3505 hom., cov: 31)
• Consequence: ENSG00000283384 ENST00000636252.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 2 publications found

Genes affected

ENSG00000283384 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370355	XR_007063863.1	n.442+4935C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283384	ENST00000636252.1	n.125+4935C>T		intron_variant	Intron 1 of 3	5
ENSG00000283384	ENST00000637731.1	n.219+4935C>T		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30613 AN: 151880 Hom.: 3505 Cov.: 31

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.0585

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.201 AC: 30601 AN: 151998 Hom.: 3505 Cov.: 31 AF XY: 0.205 AC XY: 15234 AN XY: 74268

African (AFR) AF: 0.108 AC: 4495 AN: 41484

American (AMR) AF: 0.161 AC: 2463 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 872 AN: 3472

East Asian (EAS) AF: 0.0577 AC: 298 AN: 5168

South Asian (SAS) AF: 0.266 AC: 1282 AN: 4814

European-Finnish (FIN) AF: 0.347 AC: 3654 AN: 10530

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16653 AN: 67946

Other (OTH) AF: 0.197 AC: 414 AN: 2104

Alfa AF: 0.232 Hom.: 3233

Bravo AF: 0.183

Asia WGS AF: 0.159 AC: 554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.040
DANN	Benign	0.36
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7333523; hg19: chr13-108992855; COSMIC: COSV70608511; COSMIC: COSV70608511;