rs13186787

chr5-154347209-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_198321.4(GALNT10):c.568+17471A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0188 in 479,186 control chromosomes in the GnomAD database, including 118 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 0.014 (26 hom., cov: 29)
  • Exomes 𝑓: 0.021 (92 hom.)
• Consequence: GALNT10 NM_198321.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.803

Genes affected

GALNT10 (HGNC:19873): (polypeptide N-acetylgalactosaminyltransferase 10) This gene encodes a member of the GalNAc polypeptide N-acetylgalactosaminyltransferases. These enzymes catalyze the first step in the synthesis of mucin-type oligosaccharides. These proteins transfer GalNAc from UDP-GalNAc to either serine or threonine residues of polypeptide acceptors. The protein encoded by this locus may have increased catalytic activity toward glycosylated peptides compared to activity toward non-glycosylated peptides.[provided by RefSeq, Apr 2010]

MIR1294 (HGNC:35287): (microRNA 1294) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

(HGNC:):

SAP30L-AS1 (HGNC:26760): (SAP30L antisense RNA 1 (head to head))

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0144 (2146/149032) while in subpopulation SAS AF= 0.0308 (138/4484). AF 95% confidence interval is 0.0266. There are 26 homozygotes in gnomad4. There are 990 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 26 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALNT10	NM_198321.4	c.568+17471A>G		intron_variant		ENST00000297107.11
MIR1294	NR_031626.1	n.104A>G		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALNT10	ENST00000297107.11	c.568+17471A>G		intron_variant		1	NM_198321.4	P1
MIR1294	ENST00000408503.1	n.104A>G		non_coding_transcript_exon_variant	1/1
	ENST00000657704.1	n.1118-13A>G		splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant
SAP30L-AS1	ENST00000658072.1	n.202-17252T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0144 AC: 2147 AN: 148908 Hom.: 26 Cov.: 29

Gnomad AFR AF: 0.00374

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0111

Gnomad ASJ AF: 0.00639

Gnomad EAS AF: 0.000211

Gnomad SAS AF: 0.0305

Gnomad FIN AF: 0.0102

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.0228

Gnomad OTH AF: 0.0117

GnomAD3 exomes AF: 0.0187 AC: 3623 AN: 193712 Hom.: 51 AF XY: 0.0201 AC XY: 2153 AN XY: 107176

Gnomad AFR exome AF: 0.00393

Gnomad AMR exome AF: 0.00972

Gnomad ASJ exome AF: 0.00992

Gnomad EAS exome AF: 0.0000850

Gnomad SAS exome AF: 0.0316

Gnomad FIN exome AF: 0.0122

Gnomad NFE exome AF: 0.0239

Gnomad OTH exome AF: 0.0215

GnomAD4 exome AF: 0.0208 AC: 6864 AN: 330154 Hom.: 92 Cov.: 0 AF XY: 0.0219 AC XY: 4182 AN XY: 191212

Gnomad4 AFR exome AF: 0.00379

Gnomad4 AMR exome AF: 0.00887

Gnomad4 ASJ exome AF: 0.00973

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0306

Gnomad4 FIN exome AF: 0.0129

Gnomad4 NFE exome AF: 0.0228

Gnomad4 OTH exome AF: 0.0213

GnomAD4 genome AF: 0.0144 AC: 2146 AN: 149032 Hom.: 26 Cov.: 29 AF XY: 0.0136 AC XY: 990 AN XY: 72854

Gnomad4 AFR AF: 0.00373

Gnomad4 AMR AF: 0.0110

Gnomad4 ASJ AF: 0.00639

Gnomad4 EAS AF: 0.000212

Gnomad4 SAS AF: 0.0308

Gnomad4 FIN AF: 0.0102

Gnomad4 NFE AF: 0.0228

Gnomad4 OTH AF: 0.0111

Alfa AF: 0.0173 Hom.: 16

Bravo AF: 0.0135

Asia WGS AF: 0.00577 AC: 20 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.3
Dann	Benign	0.31

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs13186787; hg19: chr5-153726769;