19-17555854-G-A

Variant names:

• chr19-17555854-G-A
• rs1246270631
• NM_024656.4:c.141G>A

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Moderate BP6_Moderate BP7

The NM_024656.4(COLGALT1):​c.141G>A​(p.Ser47Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000497 in 1,207,752 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000050 (0 hom.)
• Consequence: COLGALT1 NM_024656.4 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.335
• Publications: 0 publications found

Genes affected

COLGALT1 (HGNC:26182): (collagen beta(1-O)galactosyltransferase 1) The protein encoded by this gene is one of two enzymes that transfers galactose moieties to hydroxylysine residues of collagen and mannose binding lectin. This gene is constitutively expressed and encodes a soluble protein that localizes to the endoplasmic reticulum. [provided by RefSeq, Dec 2015]

COLGALT1 Gene-Disease associations (from GenCC):

• brain small vessel disease 3

  Inheritance: AR Classification: STRONG, MODERATE, LIMITED Submitted by: Ambry Genetics, ClinGen, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BP6: Variant 19-17555854-G-A is Benign according to our data. Variant chr19-17555854-G-A is described in ClinVar as Likely_benign. ClinVar VariationId is 1972711.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-0.335 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024656.4. 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
	COLGALT1	NM_024656.4	MANE Select	c.141G>A	p.Ser47Ser	synonymous	Exon 1 of 12	NP_078932.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COLGALT1	ENST00000252599.9	TSL:1 MANE Select	c.141G>A	p.Ser47Ser	synonymous	Exon 1 of 12	ENSP00000252599.3	Q8NBJ5
	COLGALT1	ENST00000886053.1		c.141G>A	p.Ser47Ser	synonymous	Exon 1 of 13	ENSP00000556112.1
	COLGALT1	ENST00000886054.1		c.141G>A	p.Ser47Ser	synonymous	Exon 1 of 14	ENSP00000556113.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000497 AC: 6 AN: 1207752 Hom.: 0 Cov.: 33 AF XY: 0.00000849 AC XY: 5 AN XY: 588858

African (AFR) AF: 0.00 AC: 0 AN: 24518

American (AMR) AF: 0.0000681 AC: 1 AN: 14676

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19068

East Asian (EAS) AF: 0.00 AC: 0 AN: 26968

South Asian (SAS) AF: 0.00 AC: 0 AN: 56936

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 29360

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3416

European-Non Finnish (NFE) AF: 0.00000406 AC: 4 AN: 984086

Other (OTH) AF: 0.0000205 AC: 1 AN: 48724

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000756

ClinVar

ClinVar submissions

Significance: Likely 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	-0.46
CADD	Benign	12
DANN	Benign	0.97
PhyloP100		-0.34
PromoterAI		0.025	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

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: rs1246270631; hg19: chr19-17666663;