chr7-152094085-T-G

Variant names:

• chr7-152094085-T-G
• rs17173334
• NM_022087.4:c.-38-105T>G

Variant summary

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

The NM_022087.4(GALNT11):​c.-38-105T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0408 in 875,728 control chromosomes in the GnomAD database, including 1,663 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 0.044 (266 hom., cov: 32)
  • Exomes 𝑓: 0.040 (1397 hom.)
• Consequence: GALNT11 NM_022087.4 intron
• Scores: Splicing: ADA: 0.00005159
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.801
• Publications: 4 publications found

Genes affected

GALNT11 (HGNC:19875): (polypeptide N-acetylgalactosaminyltransferase 11) Enables Notch binding activity and polypeptide N-acetylgalactosaminyltransferase activity. Involved in protein O-linked glycosylation via threonine. Predicted to be located in Golgi 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT11	NM_022087.4	c.-38-105T>G		intron_variant	Intron 1 of 11	ENST00000430044.7	NP_071370.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT11	ENST00000430044.7	c.-38-105T>G		intron_variant	Intron 1 of 11	5	NM_022087.4	ENSP00000395122.2

Frequencies

GnomAD3 genomes AF: 0.0445 AC: 6770 AN: 152184 Hom.: 267 Cov.: 32

Gnomad AFR AF: 0.0601

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0541

Gnomad ASJ AF: 0.0282

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0294

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0192

Gnomad OTH AF: 0.0372

GnomAD4 exome AF: 0.0400 AC: 28962 AN: 723426 Hom.: 1397 Cov.: 9 AF XY: 0.0422 AC XY: 15764 AN XY: 373292

African (AFR) AF: 0.0625 AC: 1134 AN: 18132

American (AMR) AF: 0.0764 AC: 1966 AN: 25718

Ashkenazi Jewish (ASJ) AF: 0.0288 AC: 457 AN: 15882

East Asian (EAS) AF: 0.205 AC: 7264 AN: 35510

South Asian (SAS) AF: 0.110 AC: 5924 AN: 53688

European-Finnish (FIN) AF: 0.0269 AC: 1106 AN: 41058

Middle Eastern (MID) AF: 0.0374 AC: 137 AN: 3664

European-Non Finnish (NFE) AF: 0.0195 AC: 9644 AN: 494646

Other (OTH) AF: 0.0379 AC: 1330 AN: 35128

GnomAD4 genome AF: 0.0445 AC: 6774 AN: 152302 Hom.: 266 Cov.: 32 AF XY: 0.0471 AC XY: 3510 AN XY: 74456

African (AFR) AF: 0.0600 AC: 2496 AN: 41572

American (AMR) AF: 0.0544 AC: 832 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0282 AC: 98 AN: 3470

East Asian (EAS) AF: 0.202 AC: 1047 AN: 5172

South Asian (SAS) AF: 0.123 AC: 595 AN: 4826

European-Finnish (FIN) AF: 0.0294 AC: 312 AN: 10612

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0192 AC: 1307 AN: 68030

Other (OTH) AF: 0.0364 AC: 77 AN: 2116

Alfa AF: 0.0284 Hom.: 188

Bravo AF: 0.0473

Asia WGS AF: 0.160 AC: 556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.1
DANN	Benign	0.54
PhyloP100		0.80
PromoterAI		-0.0079	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000052
dbscSNV1_RF	Benign	0.0060
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: rs17173334; hg19: chr7-151791170;