chr13-109801260-G-T

Position:

• chr13-109801260-G-T

Variant summary

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

The ENST00000615635.1(ENSG00000275741):​n.116-5797G>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 0.828 in 152,128 control chromosomes in the GnomAD database, including 52,254 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 0.83 (52254 hom., cov: 33)
• Consequence: ENST00000615635.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.524

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370360	XR_931723.3	n.200+4091G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000615635.1	n.116-5797G>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.828 AC: 125847 AN: 152010 Hom.: 52206 Cov.: 33

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.823

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.859

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.823

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

GnomAD4 genome AF: 0.828 AC: 125952 AN: 152128 Hom.: 52254 Cov.: 33 AF XY: 0.828 AC XY: 61566 AN XY: 74364

Gnomad4 AFR AF: 0.820

Gnomad4 AMR AF: 0.860

Gnomad4 ASJ AF: 0.859

Gnomad4 EAS AF: 0.677

Gnomad4 SAS AF: 0.776

Gnomad4 FIN AF: 0.849

Gnomad4 NFE AF: 0.836

Gnomad4 OTH AF: 0.821

Alfa AF: 0.827 Hom.: 19310

Bravo AF: 0.829

Asia WGS AF: 0.730 AC: 2504 AN: 3430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
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: rs7986346; hg19: chr13-110453607;