rs3823646

Variant names:

• chr7-100159989-G-A
• rs3823646
• NM_024637.5:c.1400C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-100159989-G-A
• chr7-100159989-G-C

Variant summary

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

The NM_024637.5(GAL3ST4):​c.1400C>T​(p.Ala467Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 1,612,990 control chromosomes in the GnomAD database, including 243,292 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 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 0.50 (19675 hom., cov: 30)
  • Exomes 𝑓: 0.55 (223617 hom.)
• Consequence: GAL3ST4 NM_024637.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.527
• Publications: 37 publications found

Genes affected

GAL3ST4 (HGNC:24145): (galactose-3-O-sulfotransferase 4) This gene encodes a member of the galactose-3-O-sulfotransferase protein family. The product of this gene catalyzes sulfonation by transferring a sulfate to the C-3' position of galactose residues in O-linked glycoproteins. This enzyme is highly specific for core 1 structures, with asialofetuin, Gal-beta-1,3-GalNAc and Gal-beta-1,3 (GlcNAc-beta-1,6)GalNAc being good substrates. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (MetaRNN=6.1614282E-6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GAL3ST4	NM_024637.5	c.1400C>T	p.Ala467Val	missense_variant	Exon 4 of 4	ENST00000360039.9	NP_078913.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GAL3ST4	ENST00000360039.9	c.1400C>T	p.Ala467Val	missense_variant	Exon 4 of 4	1	NM_024637.5	ENSP00000353142.4

Frequencies

GnomAD3 genomes AF: 0.501 AC: 75970 AN: 151700 Hom.: 19661 Cov.: 30

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.512

GnomAD2 exomes AF: 0.540 AC: 135577 AN: 250978 AF XY: 0.550

Gnomad AFR exome AF: 0.371

Gnomad AMR exome AF: 0.445

Gnomad ASJ exome AF: 0.611

Gnomad EAS exome AF: 0.644

Gnomad FIN exome AF: 0.565

Gnomad NFE exome AF: 0.551

Gnomad OTH exome AF: 0.552

GnomAD4 exome AF: 0.551 AC: 805340 AN: 1461172 Hom.: 223617 Cov.: 48 AF XY: 0.555 AC XY: 403087 AN XY: 726918

African (AFR) AF: 0.362 AC: 12108 AN: 33464

American (AMR) AF: 0.448 AC: 20028 AN: 44664

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 15905 AN: 26108

East Asian (EAS) AF: 0.608 AC: 24135 AN: 39696

South Asian (SAS) AF: 0.598 AC: 51570 AN: 86228

European-Finnish (FIN) AF: 0.561 AC: 29943 AN: 53412

Middle Eastern (MID) AF: 0.614 AC: 3537 AN: 5758

European-Non Finnish (NFE) AF: 0.553 AC: 614900 AN: 1111474

Other (OTH) AF: 0.550 AC: 33214 AN: 60368

GnomAD4 genome AF: 0.501 AC: 76025 AN: 151818 Hom.: 19675 Cov.: 30 AF XY: 0.505 AC XY: 37423 AN XY: 74174

African (AFR) AF: 0.372 AC: 15416 AN: 41386

American (AMR) AF: 0.452 AC: 6892 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2140 AN: 3464

East Asian (EAS) AF: 0.641 AC: 3300 AN: 5150

South Asian (SAS) AF: 0.597 AC: 2864 AN: 4796

European-Finnish (FIN) AF: 0.572 AC: 6030 AN: 10538

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.553 AC: 37539 AN: 67936

Other (OTH) AF: 0.512 AC: 1077 AN: 2104

Alfa AF: 0.541 Hom.: 100272

Bravo AF: 0.488

TwinsUK AF: 0.564 AC: 2093

ALSPAC AF: 0.549 AC: 2116

ESP6500AA AF: 0.386 AC: 1699

ESP6500EA AF: 0.568 AC: 4887

ExAC AF: 0.537 AC: 65198

Asia WGS AF: 0.606 AC: 2105 AN: 3478

EpiCase AF: 0.556

EpiControl AF: 0.567

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.22
BayesDel_addAF	Benign	-0.69	T
BayesDel_noAF	Benign	-0.61
CADD	Benign	22
DANN	Uncertain	1.0
DEOGEN2	Benign	0.0038	T;T
Eigen	Benign	-0.23
Eigen_PC	Benign	-0.055
FATHMM_MKL	Uncertain	0.83	D
LIST_S2	Benign	0.60	.;T
MetaRNN	Benign	0.0000062	T;T
MetaSVM	Benign	-0.98	T
MutationAssessor	Benign	1.6	L;L
PhyloP100		0.53
PrimateAI	Benign	0.38	T
PROVEAN	Benign	-0.97	N;N
REVEL	Benign	0.024
Sift	Benign	0.041	D;D
Sift4G	Benign	0.11	T;T
Polyphen		0.0080	B;B
Vest4		0.027
MPC		0.11
ClinPred		0.0096	T
GERP RS		5.0
Varity_R		0.082
gMVP		0.46
Mutation Taster		=99/1	polymorphism (auto)

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: rs3823646; hg19: chr7-99757612; COSMIC: COSV57586416; COSMIC: COSV57586416;