rs1488665

Variant names:

• chr11-45506566-T-A
• rs1488665
• ENST00000527642.5:n.496-16795A>T

Your query was ambiguous. Multiple possible variants found:

• chr11-45506566-T-A
• chr11-45506566-T-C
• chr11-45506566-T-G

Variant summary

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

The ENST00000527642.5(ENSG00000254746):​n.496-16795A>T 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: 34)
• Consequence: ENSG00000254746 ENST00000527642.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.948
• Publications: 6 publications found

Genes affected

ENSG00000254746 (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=-1.02).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376654	XR_001748204.3	n.712-16795A>T		intron_variant	Intron 4 of 4
LOC105376654	XR_931245.4	n.369-16795A>T		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254746	ENST00000527642.5	n.496-16795A>T		intron_variant	Intron 5 of 5	4
ENSG00000255041	ENST00000528445.1	n.530+6707A>T		intron_variant	Intron 1 of 2	5
ENSG00000254746	ENST00000533315.5	n.491-16795A>T		intron_variant	Intron 4 of 4	4

Frequencies

GnomAD3 genomes Cov.: 34

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

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.13
DANN	Benign	0.23
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs1488665; hg19: chr11-45528116;