rs725231

Positions:

• chr2-153772722-A-C
• chr2-153772722-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047443120.1(GALNT13):​c.-177+39892A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 152,086 control chromosomes in the GnomAD database, including 15,518 homozygotes. 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: 𝑓 0.43 (15518 hom., cov: 32)
• Consequence: GALNT13 XM_047443120.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639

Genes affected

GALNT13 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GALNT13	XM_047443120.1	c.-177+39892A>C		intron_variant			XP_047299076.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65446 AN: 151968 Hom.: 15493 Cov.: 32

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.431 AC: 65528 AN: 152086 Hom.: 15518 Cov.: 32 AF XY: 0.422 AC XY: 31382 AN XY: 74328

Gnomad4 AFR AF: 0.622

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.0999

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.384

Alfa AF: 0.300 Hom.: 1011

Bravo AF: 0.440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.067
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs725231; hg19: chr2-154629235;