rs9949617

Variant names:

• chr18-23299253-C-T
• rs9949617
• NM_032933.6:c.831-1186G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032933.6(SLC35D4):​c.831-1186G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,136 control chromosomes in the GnomAD database, including 4,121 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 0.22 (4121 hom., cov: 32)
• Consequence: SLC35D4 NM_032933.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.11
• Publications: 14 publications found

Genes affected

SLC35D4 (HGNC:31723): (transmembrane protein 241) Predicted to enable antiporter activity. Predicted to be involved in carbohydrate transport and 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032933.6. 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
	SLC35D4	NM_032933.6	MANE Select	c.831-1186G>A		intron	N/A	NP_116322.3
	SLC35D4	NM_001318834.2		c.468-1186G>A		intron	N/A	NP_001305763.1
	SLC35D4	NR_134875.2		n.891-1186G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM241	ENST00000383233.8	TSL:1 MANE Select	c.831-1186G>A		intron	N/A	ENSP00000372720.3	Q24JQ0-1
	TMEM241	ENST00000542162.5	TSL:1	c.*496-1186G>A		intron	N/A	ENSP00000440152.2	F5GXY7
	TMEM241	ENST00000473688.5	TSL:1	n.*302-1186G>A		intron	N/A	ENSP00000431584.1	Q24JQ0-2

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33231 AN: 152016 Hom.: 4111 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.219 AC: 33283 AN: 152136 Hom.: 4121 Cov.: 32 AF XY: 0.221 AC XY: 16411 AN XY: 74384

African (AFR) AF: 0.319 AC: 13249 AN: 41468

American (AMR) AF: 0.309 AC: 4716 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 841 AN: 3470

East Asian (EAS) AF: 0.167 AC: 865 AN: 5184

South Asian (SAS) AF: 0.170 AC: 819 AN: 4810

European-Finnish (FIN) AF: 0.136 AC: 1441 AN: 10600

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10633 AN: 67998

Other (OTH) AF: 0.234 AC: 494 AN: 2114

Alfa AF: 0.181 Hom.: 11855

Bravo AF: 0.237

Asia WGS AF: 0.185 AC: 644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.0030
DANN	Benign	0.35
PhyloP100		-4.1
Mutation Taster		=100/0	polymorphism (auto)

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: rs9949617; hg19: chr18-20879217;