chr13-108340507-C-T

Position:

• chr13-108340507-C-T

Variant summary

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

The ENST00000636252.1(ENSG00000283384):​n.125+4935C>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 0.201 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: ENST00000636252.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105370355	XR_007063863.1	n.442+4935C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000636252.1	n.125+4935C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000637731.1	n.219+4935C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.0577

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.197

Alfa AF: 0.234 Hom.: 2431

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

Splicing

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

Publications

LitVar

Other links and lift over

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