chr7-152113391-A-G

Variant names:

• chr7-152113391-A-G
• rs73161885
• NM_022087.4:c.1226A>G

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_022087.4(GALNT11):​c.1226A>G​(p.Glu409Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00942 in 1,613,460 control chromosomes in the GnomAD database, including 111 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 0.0093 (11 hom., cov: 32)
  • Exomes 𝑓: 0.0094 (100 hom.)
• Consequence: GALNT11 NM_022087.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.29
• Publications: 5 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]

ENSG00000310074 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.010952532).
• BS2: High Homozygotes in GnomAd4 at 11 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022087.4. 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
	GALNT11	NM_022087.4	MANE Select	c.1226A>G	p.Glu409Gly	missense	Exon 8 of 12	NP_071370.2
	GALNT11	NM_001371464.1		c.1226A>G	p.Glu409Gly	missense	Exon 8 of 12	NP_001358393.1
	GALNT11	NM_001371458.1		c.1226A>G	p.Glu409Gly	missense	Exon 9 of 13	NP_001358387.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT11	ENST00000430044.7	TSL:5 MANE Select	c.1226A>G	p.Glu409Gly	missense	Exon 8 of 12	ENSP00000395122.2
	GALNT11	ENST00000434507.6	TSL:2	c.1226A>G	p.Glu409Gly	missense	Exon 10 of 14	ENSP00000416787.1
	GALNT11	ENST00000431940.1	TSL:3	n.146A>G		non_coding_transcript_exon	Exon 1 of 4	ENSP00000390247.1

Frequencies

GnomAD3 genomes AF: 0.00931 AC: 1417 AN: 152190 Hom.: 11 Cov.: 32

Gnomad AFR AF: 0.00166

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00582

Gnomad ASJ AF: 0.00230

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00145

Gnomad FIN AF: 0.0417

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0117

Gnomad OTH AF: 0.00430

GnomAD2 exomes AF: 0.00922 AC: 2306 AN: 250150 AF XY: 0.00911

Gnomad AFR exome AF: 0.00136

Gnomad AMR exome AF: 0.00323

Gnomad ASJ exome AF: 0.00139

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.0396

Gnomad NFE exome AF: 0.0106

Gnomad OTH exome AF: 0.00858

GnomAD4 exome AF: 0.00943 AC: 13785 AN: 1461152 Hom.: 100 Cov.: 30 AF XY: 0.00934 AC XY: 6789 AN XY: 726846

African (AFR) AF: 0.00117 AC: 39 AN: 33426

American (AMR) AF: 0.00287 AC: 128 AN: 44602

Ashkenazi Jewish (ASJ) AF: 0.00165 AC: 43 AN: 26120

East Asian (EAS) AF: 0.00 AC: 0 AN: 39678

South Asian (SAS) AF: 0.00171 AC: 147 AN: 86042

European-Finnish (FIN) AF: 0.0360 AC: 1924 AN: 53408

Middle Eastern (MID) AF: 0.000694 AC: 4 AN: 5764

European-Non Finnish (NFE) AF: 0.00997 AC: 11087 AN: 1111736

Other (OTH) AF: 0.00684 AC: 413 AN: 60376

GnomAD4 genome AF: 0.00930 AC: 1416 AN: 152308 Hom.: 11 Cov.: 32 AF XY: 0.0101 AC XY: 753 AN XY: 74466

African (AFR) AF: 0.00166 AC: 69 AN: 41568

American (AMR) AF: 0.00582 AC: 89 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.00230 AC: 8 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.00145 AC: 7 AN: 4828

European-Finnish (FIN) AF: 0.0417 AC: 442 AN: 10604

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0116 AC: 792 AN: 68030

Other (OTH) AF: 0.00425 AC: 9 AN: 2116

Alfa AF: 0.00884 Hom.: 12

Bravo AF: 0.00569

TwinsUK AF: 0.00944 AC: 35

ALSPAC AF: 0.00986 AC: 38

ESP6500AA AF: 0.00204 AC: 9

ESP6500EA AF: 0.00744 AC: 64

ExAC AF: 0.00856 AC: 1039

Asia WGS AF: 0.00260 AC: 10 AN: 3478

EpiCase AF: 0.00740

EpiControl AF: 0.00653

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.079	T
BayesDel_noAF	Uncertain	0.13
CADD	Benign	23
DANN	Uncertain	1.0
DEOGEN2	Benign	0.22	T
Eigen	Benign	0.16
Eigen_PC	Uncertain	0.30
FATHMM_MKL	Uncertain	0.92	D
LIST_S2	Uncertain	0.87	D
MetaRNN	Benign	0.011	T
MetaSVM	Benign	-0.72	T
MutationAssessor	Uncertain	2.1	M
PhyloP100		5.3
PrimateAI	Uncertain	0.50	T
PROVEAN	Uncertain	-4.3	D
REVEL	Uncertain	0.37
Sift	Benign	0.099	T
Sift4G	Benign	0.10	T
Polyphen		0.044	B
Vest4		0.48
MVP		0.71
MPC		0.31
ClinPred		0.026	T
GERP RS		5.6
Varity_R		0.33
gMVP		0.85
Mutation Taster		=83/17	polymorphism

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: rs73161885; hg19: chr7-151810476;