13-108385613-C-T

Variant names:

• chr13-108385613-C-T
• rs7318477
• ENST00000636252.1:n.333+10901C>T

Variant summary

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

The ENST00000636252.1(ENSG00000283384):​n.333+10901C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 151,980 control chromosomes in the GnomAD database, including 5,365 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 0.25 (5365 hom., cov: 32)
• Consequence: ENSG00000283384 ENST00000636252.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.469
• Publications: 8 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.608 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
ENSG00000283384	ENST00000636252.1	n.333+10901C>T		intron_variant	Intron 3 of 3	5
ENSG00000283384	ENST00000637731.1	n.475+16300C>T		intron_variant	Intron 4 of 4	5

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37743 AN: 151862 Hom.: 5365 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.248 AC: 37756 AN: 151980 Hom.: 5365 Cov.: 32 AF XY: 0.255 AC XY: 18909 AN XY: 74274

African (AFR) AF: 0.312 AC: 12910 AN: 41434

American (AMR) AF: 0.198 AC: 3023 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 533 AN: 3468

East Asian (EAS) AF: 0.626 AC: 3222 AN: 5146

South Asian (SAS) AF: 0.201 AC: 973 AN: 4830

European-Finnish (FIN) AF: 0.352 AC: 3709 AN: 10538

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12741 AN: 67976

Other (OTH) AF: 0.233 AC: 491 AN: 2108

Alfa AF: 0.205 Hom.: 14855

Bravo AF: 0.244

Asia WGS AF: 0.423 AC: 1467 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.95
DANN	Benign	0.41
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs7318477; hg19: chr13-109037961;