rs12857529

Variant names:

• chr13-109787247-A-C
• rs12857529
• XM_047430835.1:c.155A>C

Your query was ambiguous. Multiple possible variants found:

• chr13-109787247-A-C
• chr13-109787247-A-G
• chr13-109787247-A-T

Variant summary

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

The XM_047430835.1(LOC124903211):​c.155A>C​(p.Asn52Thr) 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: 33)
• Consequence: LOC124903211 XM_047430835.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350
• Publications: 0 publications found

Genes affected

LOC124903211 (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=-0.79).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903211	XM_047430835.1	c.155A>C	p.Asn52Thr	missense_variant	Exon 1 of 2		XP_047286791.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000275741	ENST00000615635.1	n.115+1302A>C		intron_variant	Intron 1 of 2	4
ENSG00000275741	ENST00000772402.1	n.67+1302A>C		intron_variant	Intron 1 of 1
ENSG00000300524	ENST00000772577.1	n.70-353A>C		intron_variant	Intron 1 of 1
ENSG00000300524	ENST00000772578.1	n.-7A>C		upstream_gene_variant

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	11
DANN	Benign	0.53
PhyloP100		0.035

Splicing

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

Other links and lift over

dbSNP: rs12857529; hg19: chr13-110439594;