ENST00000507897.5:n.*61-4641T>C

Variant names:

• chr6-87472721-T-C
• rs2273129
• ENST00000507897.5:n.*61-4641T>C

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000507897.5(ENSG00000213204):​n.*61-4641T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 152,124 control chromosomes in the GnomAD database, including 28,139 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.60 (28139 hom., cov: 33)
• Consequence: ENSG00000213204 ENST00000507897.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.01
• Publications: 10 publications found

Genes affected

ENSG00000213204 (HGNC:):

SLC35A1 (HGNC:11021): (solute carrier family 35 member A1) The protein encoded by this gene is found in the membrane of the Golgi apparatus, where it transports nucleotide sugars into the Golgi. One such nucleotide sugar is CMP-sialic acid, which is imported into the Golgi by the encoded protein and subsequently glycosylated. Defects in this gene are a cause of congenital disorder of glycosylation type 2F (CDG2F). Two transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Dec 2009]

SLC35A1 Gene-Disease associations (from GenCC):

• SLC35A1-congenital disorder of glycosylation

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia, G2P

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 6-87472721-T-C is Benign according to our data. Variant chr6-87472721-T-C is described in ClinVar as Benign. ClinVar VariationId is 1259892.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507897.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000213204	ENST00000507897.5	TSL:2	n.*61-4641T>C		intron	N/A	ENSP00000426769.1
	SLC35A1	ENST00000464978.5	TSL:2	n.91+2008T>C		intron	N/A
	ENSG00000213204	ENST00000506888.5	TSL:2	n.556-4641T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.599 AC: 91100 AN: 152006 Hom.: 28090 Cov.: 33

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.600 AC: 91210 AN: 152124 Hom.: 28139 Cov.: 33 AF XY: 0.597 AC XY: 44366 AN XY: 74372

African (AFR) AF: 0.737 AC: 30587 AN: 41520

American (AMR) AF: 0.675 AC: 10312 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1706 AN: 3472

East Asian (EAS) AF: 0.511 AC: 2631 AN: 5152

South Asian (SAS) AF: 0.563 AC: 2718 AN: 4830

European-Finnish (FIN) AF: 0.480 AC: 5085 AN: 10592

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.533 AC: 36219 AN: 67970

Other (OTH) AF: 0.588 AC: 1241 AN: 2110

Alfa AF: 0.559 Hom.: 30362

Bravo AF: 0.622

Asia WGS AF: 0.612 AC: 2126 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.7
DANN	Benign	0.46
PhyloP100		-1.0
PromoterAI		0.071	Neutral

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: rs2273129; hg19: chr6-88182439;