rs530160904

Variant names:

• chr22-30636469-G-C
• rs530160904
• NM_001001479.4:c.19G>C

Your query was ambiguous. Multiple possible variants found:

• chr22-30636469-G-C
• chr22-30636469-G-A
• chr22-30636469-G-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001001479.4(SLC35E4):​c.19G>C​(p.Glu7Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLC35E4 NM_001001479.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.524
• Publications: 0 publications found

Genes affected

SLC35E4 (HGNC:17058): (solute carrier family 35 member E4) Predicted to enable antiporter activity. Predicted to be involved in transmembrane transport. Predicted to be integral component of membrane. Predicted to be active in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.12470737).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001001479.4. 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
	SLC35E4	NM_001001479.4	MANE Select	c.19G>C	p.Glu7Gln	missense	Exon 1 of 2	NP_001001479.1	Q6ICL7-1
	SLC35E4	NM_001318370.2		c.19G>C	p.Glu7Gln	missense	Exon 1 of 3	NP_001305299.1	Q6ICL7-2
	SLC35E4	NM_001318371.2		c.19G>C	p.Glu7Gln	missense	Exon 1 of 3	NP_001305300.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC35E4	ENST00000343605.5	TSL:1 MANE Select	c.19G>C	p.Glu7Gln	missense	Exon 1 of 2	ENSP00000339626.4	Q6ICL7-1
	SLC35E4	ENST00000406566.1	TSL:1	c.19G>C	p.Glu7Gln	missense	Exon 1 of 3	ENSP00000384377.1	Q6ICL7-2
	SLC35E4	ENST00000451479.1	TSL:1	c.-54G>C		upstream_gene	N/A	ENSP00000413552.1	H7C3S2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD2 exomes AF: 0.00000795 AC: 1 AN: 125734 AF XY: 0.0000150

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.000279

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1349136 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 658306

African (AFR) AF: 0.00 AC: 0 AN: 30462

American (AMR) AF: 0.00 AC: 0 AN: 31020

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 22490

East Asian (EAS) AF: 0.00 AC: 0 AN: 35052

South Asian (SAS) AF: 0.00 AC: 0 AN: 74152

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 45886

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4394

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1050106

Other (OTH) AF: 0.00 AC: 0 AN: 55574

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

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

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.073
BayesDel_addAF	Benign	-0.14	T
BayesDel_noAF	Benign	-0.44
CADD	Benign	18
DANN	Uncertain	1.0
DEOGEN2	Benign	0.013	T
Eigen	Benign	-0.041
Eigen_PC	Benign	0.13
FATHMM_MKL	Benign	0.65	D
LIST_S2	Benign	0.65	T
M_CAP	Benign	0.0081	T
MetaRNN	Benign	0.12	T
MetaSVM	Benign	-0.94	T
MutationAssessor	Uncertain	2.1	M
PhyloP100		0.52
PrimateAI	Uncertain	0.65	T
PROVEAN	Benign	-0.22	N
REVEL	Benign	0.027
Sift	Benign	0.071	T
Sift4G	Uncertain	0.042	D
Polyphen		0.15	B
Vest4		0.065
MutPred		0.20		Gain of MoRF binding (P = 0.1049)
MVP		0.24
MPC		0.55
ClinPred		0.39	T
GERP RS		4.5
PromoterAI		-0.00040	Neutral
Varity_R		0.11
gMVP		0.43
Mutation Taster		=92/8	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: rs530160904; hg19: chr22-31032456;