rs7676941

Variant names:

• chr4-172839412-A-C
• rs7676941
• NM_001034845.3:c.923+25689A>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.923+25689A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 152,060 control chromosomes in the GnomAD database, including 11,293 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 0.31 (11293 hom., cov: 32)
• Consequence: GALNTL6 NM_001034845.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01
• 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNTL6	NM_001034845.3	c.923+25689A>C		intron_variant	Intron 7 of 12	ENST00000506823.6	NP_001030017.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNTL6	ENST00000506823.6	c.923+25689A>C		intron_variant	Intron 7 of 12	1	NM_001034845.3	ENSP00000423313.1
GALNTL6	ENST00000508122.5	c.872+25689A>C		intron_variant	Intron 6 of 11	1		ENSP00000423827.1

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47179 AN: 151942 Hom.: 11269 Cov.: 32

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.311 AC: 47252 AN: 152060 Hom.: 11293 Cov.: 32 AF XY: 0.312 AC XY: 23214 AN XY: 74338

African (AFR) AF: 0.666 AC: 27601 AN: 41446

American (AMR) AF: 0.314 AC: 4797 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 548 AN: 3472

East Asian (EAS) AF: 0.280 AC: 1449 AN: 5176

South Asian (SAS) AF: 0.221 AC: 1059 AN: 4802

European-Finnish (FIN) AF: 0.201 AC: 2127 AN: 10560

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8865 AN: 67988

Other (OTH) AF: 0.252 AC: 532 AN: 2112

Alfa AF: 0.244 Hom.: 1175

Bravo AF: 0.333

Asia WGS AF: 0.303 AC: 1055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.48
PhyloP100		-2.0
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: rs7676941; hg19: chr4-173760563;