XR_007063870.1:n.2619C>T

Variant names:

• chr13-109590670-G-A
• rs914270
• XR_007063870.1:n.2619C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The XR_007063870.1(LOC124903210):​n.2619C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: LOC124903210 XR_007063870.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900
• Publications: 4 publications found

Genes affected

LOC124903210 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903210	XR_007063870.1	n.2619C>T		non_coding_transcript_exon_variant	Exon 2 of 2
LOC101927627	XR_007063867.1	n.77+152G>A		intron_variant	Intron 1 of 3
LOC101927627	XR_007063868.1	n.64+152G>A		intron_variant	Intron 1 of 4
LOC101927627	XR_007063869.1	n.77+152G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285534	ENST00000650264.1	n.759-19512C>T		intron_variant	Intron 1 of 3
ENSG00000296995	ENST00000744136.1	n.227+152G>A		intron_variant	Intron 1 of 4
ENSG00000296995	ENST00000744137.1	n.222+152G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 469

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.88
DANN	Benign	0.62
PhyloP100		-0.0090

Splicing

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

Other links and lift over

dbSNP: rs914270; hg19: chr13-110243017;