Variant chr5-177600404-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_007255.3(B4GALT7):c.50+144T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0986 in 600,386 control chromosomes in the GnomAD database, including 4,340 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.095 ( 1094 hom., cov: 31)

Exomes 𝑓: 0.10 ( 3246 hom. )

Consequence

B4GALT7
NM_007255.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.441

Variant links:

Genes affected

B4GALT7 (HGNC:930): (beta-1,4-galactosyltransferase 7) This gene is a member of the beta-1,4-galactosyltransferase (beta4GalT) family. Family members encode type II membrane-bound glycoproteins that appear to have exclusive specificity for the donor substrate UDP-galactose. Each beta4GalT member has a distinct function in the biosynthesis of different glycoconjugates and saccharide structures. As type II membrane proteins, they have an N-terminal hydrophobic signal sequence that directs the protein to the Golgi apparatus which then remains uncleaved to function as a transmembrane anchor. The enzyme encoded by this gene attaches the first galactose in the common carbohydrate-protein linkage (GlcA-beta1,3-Gal-beta1,3-Gal-beta1,4-Xyl-beta1-O-Ser) found in proteoglycans. This enzyme differs from other beta4GalTs because it lacks the conserved Cys residues found in beta4GalT1-beta4GalT6 and it is located in cis-Golgi instead of trans-Golgi. Mutations in this gene have been associated with the progeroid form of Ehlers-Danlos syndrome. [provided by RefSeq, Oct 2009]

B4GALT7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 5-177600404-T-C is Benign according to our data. Variant chr5-177600404-T-C is described in ClinVar as [Benign]. Clinvar id is 1246191.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
B4GALT7	NM_007255.3 linkuse as main transcript	c.50+144T>C	intron_variant		ENST00000029410.10
B4GALT7	XM_047416680.1 linkuse as main transcript	c.-2082T>C	5_prime_UTR_variant	1/6
B4GALT7	XM_047416681.1 linkuse as main transcript	c.-1061+144T>C	intron_variant
B4GALT7	XM_047416682.1 linkuse as main transcript	c.-346+144T>C	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
B4GALT7	ENST00000029410.10 linkuse as main transcript	c.50+144T>C		intron_variant		1	NM_007255.3	P1

Frequencies

GnomAD3 genomes

AF:

0.0949

AC:

14424

AN:

151974

Hom.:

1091

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0236

Gnomad AMI

AF:

0.0800

Gnomad AMR

AF:

0.193

Gnomad ASJ

AF:

0.265

Gnomad EAS

AF:

0.308

Gnomad SAS

AF:

0.118

Gnomad FIN

AF:

0.112

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.0863

Gnomad OTH

AF:

0.120

GnomAD4 exome

AF:

0.0999

AC:

44796

AN:

448294

Hom.:

3246

AF XY:

0.100

AC XY:

22160

AN XY:

221702

show subpopulations

Gnomad4 AFR exome

AF:

0.0232

Gnomad4 AMR exome

AF:

0.179

Gnomad4 ASJ exome

AF:

0.251

Gnomad4 EAS exome

AF:

0.322

Gnomad4 SAS exome

AF:

0.101

Gnomad4 FIN exome

AF:

0.117

Gnomad4 NFE exome

AF:

0.0795

Gnomad4 OTH exome

AF:

0.121

GnomAD4 genome

AF:

0.0949

AC:

14432

AN:

152092

Hom.:

1094

Cov.:

AF XY:

0.0997

AC XY:

7409

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.0236

Gnomad4 AMR

AF:

0.193

Gnomad4 ASJ

AF:

0.265

Gnomad4 EAS

AF:

0.307

Gnomad4 SAS

AF:

0.117

Gnomad4 FIN

AF:

0.112

Gnomad4 NFE

AF:

0.0863

Gnomad4 OTH

AF:

0.125

Alfa

AF:

0.100

Hom.:

1114

Bravo

AF:

0.102

Asia WGS

AF:

0.239

AC:

828

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 26, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

7.8

DANN

Benign

0.84

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over