chr2-31137814-T-A

Variant names:

• chr2-31137814-T-A
• rs2008535
• NM_024572.4:c.129+144A>T

Variant summary

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

The NM_001253826.2(GALNT14):​c.129+144A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 1,026,200 control chromosomes in the GnomAD database, including 37,596 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 0.28 (6098 hom., cov: 33)
  • Exomes 𝑓: 0.26 (31498 hom.)
• Consequence: GALNT14 NM_001253826.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310
• Publications: 5 publications found

Genes affected

GALNT14 (HGNC:22946): (polypeptide N-acetylgalactosaminyltransferase 14) This gene encodes a Golgi protein which is a member of the polypeptide N-acetylgalactosaminyltransferase (ppGalNAc-Ts) protein family. These enzymes catalyze the transfer of N-acetyl-D-galactosamine (GalNAc) to the hydroxyl groups on serines and threonines in target peptides. The encoded protein has been shown to transfer GalNAc to large proteins like mucins. Alterations in this gene may play a role in cancer progression and response to chemotherapy. [provided by RefSeq, Jun 2016]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001253826.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT14	NM_024572.4	MANE Select	c.129+144A>T		intron	N/A	NP_078848.2
	GALNT14	NM_001253826.2		c.129+144A>T		intron	N/A	NP_001240755.1
	GALNT14	NM_001329096.2		c.-117+144A>T		intron	N/A	NP_001316025.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT14	ENST00000349752.10	TSL:1 MANE Select	c.129+144A>T		intron	N/A	ENSP00000288988.6
	GALNT14	ENST00000464038.5	TSL:1	n.388+9108A>T		intron	N/A
	GALNT14	ENST00000324589.9	TSL:2	c.129+144A>T		intron	N/A	ENSP00000314500.5

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42807 AN: 151912 Hom.: 6082 Cov.: 33

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.274

GnomAD4 exome AF: 0.265 AC: 231241 AN: 874172 Hom.: 31498 AF XY: 0.265 AC XY: 116627 AN XY: 439696

African (AFR) AF: 0.336 AC: 6739 AN: 20040

American (AMR) AF: 0.261 AC: 5379 AN: 20572

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 4127 AN: 16266

East Asian (EAS) AF: 0.295 AC: 9679 AN: 32828

South Asian (SAS) AF: 0.299 AC: 16365 AN: 54806

European-Finnish (FIN) AF: 0.253 AC: 10470 AN: 41404

Middle Eastern (MID) AF: 0.328 AC: 1115 AN: 3402

European-Non Finnish (NFE) AF: 0.258 AC: 166460 AN: 645202

Other (OTH) AF: 0.275 AC: 10907 AN: 39652

GnomAD4 genome AF: 0.282 AC: 42853 AN: 152028 Hom.: 6098 Cov.: 33 AF XY: 0.282 AC XY: 20950 AN XY: 74306

African (AFR) AF: 0.334 AC: 13835 AN: 41464

American (AMR) AF: 0.264 AC: 4043 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 905 AN: 3472

East Asian (EAS) AF: 0.276 AC: 1416 AN: 5126

South Asian (SAS) AF: 0.297 AC: 1433 AN: 4818

European-Finnish (FIN) AF: 0.255 AC: 2697 AN: 10584

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17636 AN: 67954

Other (OTH) AF: 0.277 AC: 584 AN: 2108

Alfa AF: 0.266 Hom.: 680

Bravo AF: 0.284

Asia WGS AF: 0.277 AC: 961 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	5.2
DANN	Benign	0.87
PhyloP100		-0.031
PromoterAI		-0.059	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2008535; hg19: chr2-31360680; COSMIC: COSV61106951;