chr13-109787247-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047430835.1(LOC124903211):​c.155A>G​(p.Asn52Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.964 in 151,854 control chromosomes in the GnomAD database, including 70,791 homozygotes. 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: 𝑓 0.96 (70791 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903211	XM_047430835.1	c.155A>G	p.Asn52Ser	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>G		intron_variant	Intron 1 of 2	4
ENSG00000275741	ENST00000772402.1	n.67+1302A>G		intron_variant	Intron 1 of 1
ENSG00000300524	ENST00000772577.1	n.70-353A>G		intron_variant	Intron 1 of 1
ENSG00000300524	ENST00000772578.1	n.-7A>G		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.964 AC: 146290 AN: 151748 Hom.: 70745 Cov.: 33

Gnomad AFR AF: 0.875

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.987

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.990

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.974

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

GnomAD4 genome AF: 0.964 AC: 146390 AN: 151854 Hom.: 70791 Cov.: 33 AF XY: 0.966 AC XY: 71665 AN XY: 74202

African (AFR) AF: 0.875 AC: 36266 AN: 41450

American (AMR) AF: 0.987 AC: 15099 AN: 15298

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3472 AN: 3472

East Asian (EAS) AF: 1.00 AC: 4996 AN: 4996

South Asian (SAS) AF: 1.00 AC: 4822 AN: 4824

European-Finnish (FIN) AF: 1.00 AC: 10574 AN: 10574

Middle Eastern (MID) AF: 0.990 AC: 289 AN: 292

European-Non Finnish (NFE) AF: 1.00 AC: 67902 AN: 67924

Other (OTH) AF: 0.974 AC: 2060 AN: 2114

Alfa AF: 0.980 Hom.: 9088

Bravo AF: 0.959

Asia WGS AF: 0.990 AC: 3421 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	11
DANN	Benign	0.45
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;