rs1812424

Variant names:

• chr4-172234443-A-G
• rs1812424
• NM_001034845.3:c.247+4679A>G

Your query was ambiguous. Multiple possible variants found:

• chr4-172234443-A-G
• chr4-172234443-A-T

Variant summary

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

The NM_001034845.3(GALNTL6):​c.247+4679A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 152,002 control chromosomes in the GnomAD database, including 11,145 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 0.38 (11145 hom., cov: 33)
• Consequence: GALNTL6 NM_001034845.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001034845.3. 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
	GALNTL6	NM_001034845.3	MANE Select	c.247+4679A>G		intron	N/A	NP_001030017.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNTL6	ENST00000506823.6	TSL:1 MANE Select	c.247+4679A>G		intron	N/A	ENSP00000423313.1
	GALNTL6	ENST00000508122.5	TSL:1	c.196+4679A>G		intron	N/A	ENSP00000423827.1

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57722 AN: 151884 Hom.: 11141 Cov.: 33

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.400

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.380 AC: 57747 AN: 152002 Hom.: 11145 Cov.: 33 AF XY: 0.376 AC XY: 27913 AN XY: 74288

African (AFR) AF: 0.358 AC: 14834 AN: 41486

American (AMR) AF: 0.400 AC: 6116 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1739 AN: 3468

East Asian (EAS) AF: 0.138 AC: 715 AN: 5172

South Asian (SAS) AF: 0.250 AC: 1203 AN: 4818

European-Finnish (FIN) AF: 0.372 AC: 3938 AN: 10574

Middle Eastern (MID) AF: 0.396 AC: 114 AN: 288

European-Non Finnish (NFE) AF: 0.411 AC: 27919 AN: 67894

Other (OTH) AF: 0.374 AC: 790 AN: 2114

Alfa AF: 0.392 Hom.: 1477

Bravo AF: 0.382

Asia WGS AF: 0.220 AC: 761 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.78
PhyloP100		0.21
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: rs1812424; hg19: chr4-173155594;