chr3-52695669-T-TTAAA

Variant names:

• chr3-52695669-T-TTAAA
• rs140214041
• NM_018446.4:c.646-86_646-83dupTTTA

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_018446.4(GLT8D1):​c.646-86_646-83dupTTTA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0508 in 803,842 control chromosomes in the GnomAD database, including 1,257 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.061 (342 hom., cov: 31)
  • Exomes 𝑓: 0.048 (915 hom.)
• Consequence: GLT8D1 NM_018446.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.194
• Publications: 0 publications found

Genes affected

GLT8D1 (HGNC:24870): (glycosyltransferase 8 domain containing 1) This gene encodes a member of the glycosyltransferase family. The specific function of this protein has not been determined. Alternative splicing results in multiple transcript variants of this gene [provided by RefSeq, May 2013]

GNL3 (HGNC:29931): (G protein nucleolar 3) The protein encoded by this gene may interact with p53 and may be involved in tumorigenesis. The encoded protein also appears to be important for stem cell proliferation. This protein is found in both the nucleus and nucleolus. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Nov 2010]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant 3-52695669-T-TTAAA is Benign according to our data. Variant chr3-52695669-T-TTAAA is described in ClinVar as Benign. ClinVar VariationId is 1287305.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0825 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018446.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GLT8D1	NM_018446.4	MANE Select	c.646-86_646-83dupTTTA		intron	N/A	NP_060916.1	Q68CQ7-1
	GLT8D1	NM_001010983.3		c.646-86_646-83dupTTTA		intron	N/A	NP_001010983.1	Q68CQ7-1
	GLT8D1	NM_001278280.2		c.646-86_646-83dupTTTA		intron	N/A	NP_001265209.1	Q68CQ7-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GLT8D1	ENST00000266014.11	TSL:1 MANE Select	c.646-86_646-83dupTTTA		intron	N/A	ENSP00000266014.5	Q68CQ7-1
	GLT8D1	ENST00000394783.7	TSL:1	c.646-86_646-83dupTTTA		intron	N/A	ENSP00000378263.3	Q68CQ7-1
	GLT8D1	ENST00000478968.6	TSL:1	c.646-86_646-83dupTTTA		intron	N/A	ENSP00000419612.2	Q68CQ7-1

Frequencies

GnomAD3 genomes AF: 0.0608 AC: 9251 AN: 152178 Hom.: 342 Cov.: 31

Gnomad AFR AF: 0.0848

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.0510

Gnomad ASJ AF: 0.0660

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0124

Gnomad FIN AF: 0.0295

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0607

Gnomad OTH AF: 0.0703

GnomAD4 exome AF: 0.0484 AC: 31537 AN: 651546 Hom.: 915 Cov.: 8 AF XY: 0.0473 AC XY: 16279 AN XY: 344108

African (AFR) AF: 0.0870 AC: 1427 AN: 16404

American (AMR) AF: 0.0341 AC: 934 AN: 27382

Ashkenazi Jewish (ASJ) AF: 0.0589 AC: 968 AN: 16442

East Asian (EAS) AF: 0.0000560 AC: 2 AN: 35732

South Asian (SAS) AF: 0.0149 AC: 835 AN: 56190

European-Finnish (FIN) AF: 0.0318 AC: 1548 AN: 48718

Middle Eastern (MID) AF: 0.0665 AC: 261 AN: 3926

European-Non Finnish (NFE) AF: 0.0576 AC: 23847 AN: 413930

Other (OTH) AF: 0.0523 AC: 1715 AN: 32822

GnomAD4 genome AF: 0.0608 AC: 9258 AN: 152296 Hom.: 342 Cov.: 31 AF XY: 0.0587 AC XY: 4374 AN XY: 74470

African (AFR) AF: 0.0848 AC: 3523 AN: 41548

American (AMR) AF: 0.0508 AC: 778 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0660 AC: 229 AN: 3470

East Asian (EAS) AF: 0.000192 AC: 1 AN: 5196

South Asian (SAS) AF: 0.0126 AC: 61 AN: 4826

European-Finnish (FIN) AF: 0.0295 AC: 313 AN: 10618

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0607 AC: 4131 AN: 68016

Other (OTH) AF: 0.0695 AC: 147 AN: 2114

Alfa AF: 0.0606 Hom.: 40

Bravo AF: 0.0635

Asia WGS AF: 0.0160 AC: 54 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.19
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs140214041; hg19: chr3-52729685;