chr4-172220913-T-A

Variant names:

• chr4-172220913-T-A
• rs10520224
• NM_001034845.3:c.139-8743T>A

Variant summary

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

The NM_001034845.3(GALNTL6):​c.139-8743T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0403 in 151,994 control chromosomes in the GnomAD database, including 320 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 0.040 (320 hom., cov: 32)
• Consequence: GALNTL6 NM_001034845.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200
• Publications: 1 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNTL6	NM_001034845.3	c.139-8743T>A		intron_variant	Intron 2 of 12	ENST00000506823.6	NP_001030017.2
GALNTL6	XM_017008244.3	c.163-8743T>A		intron_variant	Intron 1 of 11		XP_016863733.1
GALNTL6	XM_011531993.3	c.-99-8743T>A		intron_variant	Intron 1 of 11		XP_011530295.1
GALNTL6	XM_017008243.3	c.139-8743T>A		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.139-8743T>A		intron_variant	Intron 2 of 12	1	NM_001034845.3	ENSP00000423313.1
GALNTL6	ENST00000508122.5	c.88-8743T>A		intron_variant	Intron 1 of 11	1		ENSP00000423827.1

Frequencies

GnomAD3 genomes AF: 0.0403 AC: 6117 AN: 151876 Hom.: 320 Cov.: 32

Gnomad AFR AF: 0.00922

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.0825

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0138

Gnomad FIN AF: 0.0545

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0352

Gnomad OTH AF: 0.0384

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

GnomAD4 genome AF: 0.0403 AC: 6124 AN: 151994 Hom.: 320 Cov.: 32 AF XY: 0.0415 AC XY: 3086 AN XY: 74340

African (AFR) AF: 0.00919 AC: 382 AN: 41560

American (AMR) AF: 0.150 AC: 2286 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.0825 AC: 286 AN: 3466

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5182

South Asian (SAS) AF: 0.0139 AC: 67 AN: 4834

European-Finnish (FIN) AF: 0.0545 AC: 578 AN: 10614

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0353 AC: 2390 AN: 67772

Other (OTH) AF: 0.0380 AC: 80 AN: 2108

Alfa AF: 0.0375 Hom.: 23

Bravo AF: 0.0479

Asia WGS AF: 0.0120 AC: 43 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.3
DANN	Benign	0.76
PhyloP100		-0.0020
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: rs10520224; hg19: chr4-173142064;