rs11088981

Variant names:

• chr21-43450270-C-T
• rs11088981
• XM_047441058.1:c.161C>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The XM_047441058.1(LOC124900467):​c.161C>T​(p.Ser54Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 4/4 in silico tools predict 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: 0)
• Consequence: LOC124900467 XM_047441058.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.02
• Publications: 10 publications found

Genes affected

LOC124900467 (HGNC:):

LINC00319 (HGNC:19730): (long intergenic non-protein coding RNA 319)

HSF2BP (HGNC:5226): (heat shock transcription factor 2 binding protein) HSF2 binding protein (HSF2BP) associates with HSF2. The interaction occurs between the trimerization domain of HSF2 and the amino terminal hydrophilic region of HSF2BP that comprises two leucine zipper motifs. HSF2BP may therefore be involved in modulating HSF2 activation. [provided by RefSeq, Jul 2008]

LINC00313 (HGNC:16416): (long intergenic non-protein coding RNA 313)

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900467	XM_047441058.1	c.161C>T	p.Ser54Leu	missense_variant	Exon 1 of 2		XP_047297014.1
LOC124900467	XM_047441059.1	c.161C>T	p.Ser54Leu	missense_variant	Exon 1 of 3		XP_047297015.1
LOC124900467	XM_047441060.1	c.161C>T	p.Ser54Leu	missense_variant	Exon 1 of 2		XP_047297016.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00319	ENST00000342757.3	n.247C>T		non_coding_transcript_exon_variant	Exon 1 of 3	2
LINC00319	ENST00000448049.1	n.604-469C>T		intron_variant	Intron 2 of 3	5
LINC00313	ENST00000782250.1	n.442-10391G>A		intron_variant	Intron 4 of 4
LINC00319	ENST00000651768.1	n.-136C>T		upstream_gene_variant

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 0

Alfa AF: 0.127 Hom.: 1816

Asia WGS AF: 0.137 AC: 474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.55
DANN	Benign	0.56
PhyloP100		-5.0

Splicing

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

Other links and lift over

dbSNP: rs11088981; hg19: chr21-44870150;