rs1380131

Variant names:

• chr14-53606140-C-A
• XR_007064176.1:n.4943G>T

Your query was ambiguous. Multiple possible variants found:

• chr14-53606140-C-A
• chr14-53606140-C-G
• chr14-53606140-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The XR_007064176.1(LOC124903316):​n.4943G>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: 33)
• Consequence: LOC124903316 XR_007064176.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.626

Genes affected

LOC124903316 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903316	XR_007064176.1	n.4943G>T		non_coding_transcript_exon_variant	Exon 2 of 2
LOC105370504	XR_001750974.1	n.3896-81059C>A		intron_variant	Intron 2 of 2
LOC105370504	XR_001750975.3	n.29701-81059C>A		intron_variant	Intron 2 of 2
LOC105370504	XR_943876.3	n.29701-81059C>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000225680	ENST00000436530.1	n.375-5957G>T		intron_variant	Intron 1 of 1	3
ENSG00000237356	ENST00000456100.6	n.326-81059C>A		intron_variant	Intron 3 of 3	4
ENSG00000237356	ENST00000648066.1	n.335-81059C>A		intron_variant	Intron 4 of 9

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.43
DANN	Benign	0.55

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr14-54072858;