rs714649

Variant names:

• chr2-157284580-G-A
• rs714649
• NM_014568.3:c.1621+132G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-157284580-G-A
• chr2-157284580-G-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_014568.3(GALNT5):​c.1621+132G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000258 in 690,982 control chromosomes in the GnomAD database, including 1 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 0.00021 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00027 (1 hom.)
• Consequence: GALNT5 NM_014568.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260
• Publications: 1 publications found

Genes affected

GALNT5 (HGNC:4127): (polypeptide N-acetylgalactosaminyltransferase 5) The protein encoded by this gene is a membrane-bound polypeptide N-acetylgalactosaminyltransferase that is found in the Golgi. The encoded protein catalyzes the first step in the mucin-type O-glycosylation of Golgi proteins, transfering an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. [provided by RefSeq, Aug 2016]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT5	NM_014568.3	c.1621+132G>A		intron_variant	Intron 2 of 9	ENST00000259056.5	NP_055383.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT5	ENST00000259056.5	c.1621+132G>A		intron_variant	Intron 2 of 9	1	NM_014568.3	ENSP00000259056.4

Frequencies

GnomAD3 genomes AF: 0.000210 AC: 32 AN: 152100 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0000242

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000262

Gnomad ASJ AF: 0.000864

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.000828

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000279

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000271 AC: 146 AN: 538764 Hom.: 1 AF XY: 0.000320 AC XY: 91 AN XY: 284010

African (AFR) AF: 0.00 AC: 0 AN: 14894

American (AMR) AF: 0.000141 AC: 4 AN: 28398

Ashkenazi Jewish (ASJ) AF: 0.000503 AC: 8 AN: 15910

East Asian (EAS) AF: 0.000794 AC: 25 AN: 31484

South Asian (SAS) AF: 0.000406 AC: 21 AN: 51720

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 32462

Middle Eastern (MID) AF: 0.00133 AC: 5 AN: 3750

European-Non Finnish (NFE) AF: 0.000227 AC: 75 AN: 330824

Other (OTH) AF: 0.000273 AC: 8 AN: 29322

GnomAD4 genome AF: 0.000210 AC: 32 AN: 152218 Hom.: 0 Cov.: 33 AF XY: 0.000269 AC XY: 20 AN XY: 74462

African (AFR) AF: 0.0000241 AC: 1 AN: 41478

American (AMR) AF: 0.000262 AC: 4 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.000864 AC: 3 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5192

South Asian (SAS) AF: 0.000829 AC: 4 AN: 4828

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10612

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000279 AC: 19 AN: 68024

Other (OTH) AF: 0.00 AC: 0 AN: 2112

Alfa AF: 0.00 Hom.: 93

Bravo AF: 0.000178

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.8
DANN	Benign	0.69
PhyloP100		0.026
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs714649; hg19: chr2-158141092;