13-108385613-C-T

Position:

• chr13-108385613-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000636252.1(ENSG00000283384):​n.333+10901C>T variant causes a intron, non coding transcript 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: ENST00000636252.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.469

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000636252.1	n.333+10901C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000637731.1	n.475+16300C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.626

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.233

Alfa AF: 0.197 Hom.: 6049

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7318477; hg19: chr13-109037961;