13-33013514-A-T

Variant names:

• chr13-33013514-A-T
• rs398655
• XM_047430819.1:c.729T>A

Variant summary

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

The XM_047430819.1(LOC124903151):​c.729T>A​(p.His243Gln) variant causes a missense 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. 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: 32)
• Consequence: LOC124903151 XM_047430819.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41
• Publications: 15 publications found

Genes affected

LOC124903151 (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=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903151	XM_047430819.1	c.729T>A	p.His243Gln	missense_variant	Exon 2 of 2		XP_047286775.1
LOC124903151	XR_007063749.1	n.339T>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308044	ENST00000830674.1	n.531T>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000308044	ENST00000830675.1	n.694T>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000308044	ENST00000830676.1	n.338T>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000308044	ENST00000830677.1	n.266T>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 57550

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.083
DANN	Benign	0.16
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs398655; hg19: chr13-33587652;