ENST00000425648.1:n.121+1266G>C

Variant names:

• chr14-53370767-G-C
• rs12434047
• ENST00000425648.1:n.121+1266G>C

Variant summary

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

The ENST00000425648.1(ENSG00000237356):​n.121+1266G>C variant causes a intron 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: 31)
• Consequence: ENSG00000237356 ENST00000425648.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.480

Genes affected

ENSG00000237356 (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=-0.76).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370504	XR_001750974.1	n.3895+1266G>C		intron_variant	Intron 2 of 2
LOC105370504	XR_001750975.3	n.29700+1266G>C		intron_variant	Intron 2 of 2
LOC105370504	XR_007064173.1	n.29700+1266G>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000237356	ENST00000425648.1	n.121+1266G>C		intron_variant	Intron 1 of 1	4
ENSG00000237356	ENST00000456100.6	n.325+1266G>C		intron_variant	Intron 3 of 3	4
ENSG00000237356	ENST00000648066.1	n.334+1266G>C		intron_variant	Intron 4 of 9

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.38
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12434047; hg19: chr14-53837485;