4-172000448-T-C

Variant names:

• chr4-172000448-T-C
• rs10520213
• NM_001034845.3:c.138+185730T>C

Variant summary

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

The NM_001034845.3(GALNTL6):​c.138+185730T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.955 in 152,164 control chromosomes in the GnomAD database, including 69,481 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 0.96 (69481 hom., cov: 30)
• Consequence: GALNTL6 NM_001034845.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.636
• Publications: 2 publications found

Genes affected

GALNTL6 (HGNC:33844): (polypeptide N-acetylgalactosaminyltransferase like 6) Enables polypeptide N-acetylgalactosaminyltransferase activity. Involved in protein O-linked glycosylation via threonine. Predicted to be located in Golgi membrane. 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNTL6	NM_001034845.3	c.138+185730T>C		intron_variant	Intron 2 of 12	ENST00000506823.6	NP_001030017.2
GALNTL6	XM_017008243.3	c.138+185730T>C		intron_variant	Intron 2 of 9		XP_016863732.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNTL6	ENST00000506823.6	c.138+185730T>C		intron_variant	Intron 2 of 12	1	NM_001034845.3	ENSP00000423313.1

Frequencies

GnomAD3 genomes AF: 0.955 AC: 145214 AN: 152046 Hom.: 69422 Cov.: 30

Gnomad AFR AF: 0.915

Gnomad AMI AF: 0.974

Gnomad AMR AF: 0.979

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 0.946

Gnomad SAS AF: 0.993

Gnomad FIN AF: 0.957

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.968

Gnomad OTH AF: 0.967

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.955 AC: 145333 AN: 152164 Hom.: 69481 Cov.: 30 AF XY: 0.957 AC XY: 71175 AN XY: 74394

African (AFR) AF: 0.916 AC: 38017 AN: 41516

American (AMR) AF: 0.979 AC: 14940 AN: 15256

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3471 AN: 3472

East Asian (EAS) AF: 0.946 AC: 4865 AN: 5142

South Asian (SAS) AF: 0.993 AC: 4790 AN: 4824

European-Finnish (FIN) AF: 0.957 AC: 10159 AN: 10610

Middle Eastern (MID) AF: 0.990 AC: 291 AN: 294

European-Non Finnish (NFE) AF: 0.968 AC: 65868 AN: 68024

Other (OTH) AF: 0.967 AC: 2044 AN: 2114

Alfa AF: 0.952 Hom.: 31690

Bravo AF: 0.955

Asia WGS AF: 0.959 AC: 3335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.58
PhyloP100		-0.64
Mutation Taster		=100/0	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: rs10520213; hg19: chr4-172921599;