rs3817602

Variant names:

• chr12-103996747-G-A
• rs3817602
• NM_001384711.1:c.588C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-103996747-G-A
• chr12-103996747-G-T

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_Moderate BP7 BA1

The NM_001384711.1(GLT8D2):​c.588C>T​(p.Leu196Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0352 in 1,612,234 control chromosomes in the GnomAD database, including 2,854 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 0.082 (1015 hom., cov: 32)
  • Exomes 𝑓: 0.030 (1839 hom.)
• Consequence: GLT8D2 NM_001384711.1 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.800
• Publications: 12 publications found

Genes affected

GLT8D2 (HGNC:24890): (glycosyltransferase 8 domain containing 2) Predicted to enable glycosyltransferase activity. Predicted to be integral component of membrane. Predicted to be active in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BP7: Synonymous conserved (PhyloP=-0.8 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001384711.1. 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
	GLT8D2	NM_001384711.1	MANE Select	c.588C>T	p.Leu196Leu	synonymous	Exon 8 of 11	NP_001371640.1
	GLT8D2	NM_001384712.1		c.603C>T	p.Leu201Leu	synonymous	Exon 7 of 10	NP_001371641.1
	GLT8D2	NM_001316967.2		c.588C>T	p.Leu196Leu	synonymous	Exon 8 of 11	NP_001303896.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GLT8D2	ENST00000360814.9	TSL:1 MANE Select	c.588C>T	p.Leu196Leu	synonymous	Exon 8 of 11	ENSP00000354053.4
	GLT8D2	ENST00000546436.5	TSL:5	c.588C>T	p.Leu196Leu	synonymous	Exon 7 of 10	ENSP00000449750.1
	GLT8D2	ENST00000548660.5	TSL:2	c.588C>T	p.Leu196Leu	synonymous	Exon 8 of 11	ENSP00000447450.1

Frequencies

GnomAD3 genomes AF: 0.0814 AC: 12385 AN: 152132 Hom.: 1009 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0736

Gnomad ASJ AF: 0.0680

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.0263

Gnomad FIN AF: 0.0191

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0197

Gnomad OTH AF: 0.0813

GnomAD2 exomes AF: 0.0504 AC: 12645 AN: 250692 AF XY: 0.0457

Gnomad AFR exome AF: 0.206

Gnomad AMR exome AF: 0.0590

Gnomad ASJ exome AF: 0.0665

Gnomad EAS exome AF: 0.149

Gnomad FIN exome AF: 0.0208

Gnomad NFE exome AF: 0.0209

Gnomad OTH exome AF: 0.0477

GnomAD4 exome AF: 0.0303 AC: 44281 AN: 1459984 Hom.: 1839 Cov.: 30 AF XY: 0.0300 AC XY: 21759 AN XY: 726344

African (AFR) AF: 0.208 AC: 6940 AN: 33396

American (AMR) AF: 0.0587 AC: 2617 AN: 44562

Ashkenazi Jewish (ASJ) AF: 0.0617 AC: 1610 AN: 26100

East Asian (EAS) AF: 0.169 AC: 6684 AN: 39654

South Asian (SAS) AF: 0.0256 AC: 2204 AN: 86104

European-Finnish (FIN) AF: 0.0192 AC: 1023 AN: 53398

Middle Eastern (MID) AF: 0.0798 AC: 453 AN: 5674

European-Non Finnish (NFE) AF: 0.0180 AC: 20025 AN: 1110814

Other (OTH) AF: 0.0452 AC: 2725 AN: 60282

GnomAD4 genome AF: 0.0815 AC: 12410 AN: 152250 Hom.: 1015 Cov.: 32 AF XY: 0.0814 AC XY: 6065 AN XY: 74468

African (AFR) AF: 0.202 AC: 8403 AN: 41516

American (AMR) AF: 0.0734 AC: 1123 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0680 AC: 236 AN: 3472

East Asian (EAS) AF: 0.149 AC: 769 AN: 5178

South Asian (SAS) AF: 0.0265 AC: 128 AN: 4830

European-Finnish (FIN) AF: 0.0191 AC: 203 AN: 10616

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0197 AC: 1341 AN: 68020

Other (OTH) AF: 0.0804 AC: 170 AN: 2114

Alfa AF: 0.0440 Hom.: 578

Bravo AF: 0.0919

Asia WGS AF: 0.0850 AC: 295 AN: 3478

EpiCase AF: 0.0249

EpiControl AF: 0.0254

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	0.91
DANN	Benign	0.71
PhyloP100		-0.80
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs3817602; hg19: chr12-104390525; COSMIC: COSV62563245; COSMIC: COSV62563245;