ENST00000748002.1:n.441G>T

Variant names:

• chr11-35088128-G-T
• rs1365057
• ENST00000748002.1:n.441G>T

Variant summary

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

The ENST00000748002.1(ENSG00000297460):​n.441G>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: ENSG00000297460 ENST00000748002.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.891
• Publications: 10 publications found

Genes affected

ENSG00000297460 (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=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376627	XR_001748184.2	n.99G>T		non_coding_transcript_exon_variant	Exon 1 of 3
LOC105376627	XR_931193.3	n.99G>T		non_coding_transcript_exon_variant	Exon 1 of 4
LOC105376627	XR_931194.2	n.4055-310G>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297460	ENST00000748002.1	n.441G>T		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000297460	ENST00000748003.1	n.107G>T		non_coding_transcript_exon_variant	Exon 1 of 4
ENSG00000297460	ENST00000747995.1	n.137-310G>T		intron_variant	Intron 2 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

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.74
DANN	Benign	0.58
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs1365057; hg19: chr11-35109675;