rs8187742

Variant names:

• chr15-84888762-C-T
• rs8187742
• NM_004213.5:c.97-10C>T

Your query was ambiguous. Multiple possible variants found:

• chr15-84888762-C-T
• chr15-84888762-C-A

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP6 BS1 BS2

The NM_004213.5(SLC28A1):​c.97-10C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.001 in 1,549,480 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.0051 (5 hom., cov: 32)
  • Exomes 𝑓: 0.00056 (6 hom.)
• Consequence: SLC28A1 NM_004213.5 intron
• Scores: Splicing: ADA: 0.00004090
• Clinical Significance: Likely benign no assertion criteria provided B:1
• Conservation: PhyloP100: -0.254
• Publications: 1 publications found

Genes affected

SLC28A1 (HGNC:11001): (solute carrier family 28 member 1) Enables azole transmembrane transporter activity; cytidine transmembrane transporter activity; and uridine transmembrane transporter activity. Involved in azole transmembrane transport; nucleoside transport; and pyrimidine-containing compound transmembrane transport. Located in cytosol; nuclear speck; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 15-84888762-C-T is Benign according to our data. Variant chr15-84888762-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 3056473.Status of the report is no_assertion_criteria_provided, 0 stars.
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00506 (770/152314) while in subpopulation AFR AF = 0.0173 (719/41558). AF 95% confidence interval is 0.0163. There are 5 homozygotes in GnomAd4. There are 361 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 5 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004213.5. 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
	SLC28A1	NM_004213.5	MANE Select	c.97-10C>T		intron	N/A	NP_004204.3
	SLC28A1	NM_001287762.2		c.97-10C>T		intron	N/A	NP_001274691.1	O00337-1
	SLC28A1	NM_001321722.2		c.97-10C>T		intron	N/A	NP_001308651.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC28A1	ENST00000394573.6	TSL:1 MANE Select	c.97-10C>T		intron	N/A	ENSP00000378074.1	O00337-1
	SLC28A1	ENST00000286749.3	TSL:1	c.97-10C>T		intron	N/A	ENSP00000286749.3	O00337-1
	SLC28A1	ENST00000338602.6	TSL:1	c.97-10C>T		intron	N/A	ENSP00000341629.2	O00337-2

Frequencies

GnomAD3 genomes AF: 0.00503 AC: 766 AN: 152196 Hom.: 5 Cov.: 32

Gnomad AFR AF: 0.0173

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00183

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.0000941

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000220

Gnomad OTH AF: 0.00239

GnomAD2 exomes AF: 0.00136 AC: 210 AN: 154606 AF XY: 0.000953

Gnomad AFR exome AF: 0.0192

Gnomad AMR exome AF: 0.00117

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000176

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000154

Gnomad OTH exome AF: 0.000905

GnomAD4 exome AF: 0.000560 AC: 783 AN: 1397166 Hom.: 6 Cov.: 30 AF XY: 0.000453 AC XY: 312 AN XY: 689408

African (AFR) AF: 0.0172 AC: 544 AN: 31612

American (AMR) AF: 0.00131 AC: 47 AN: 35796

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25172

East Asian (EAS) AF: 0.00 AC: 0 AN: 35784

South Asian (SAS) AF: 0.0000252 AC: 2 AN: 79218

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 49076

Middle Eastern (MID) AF: 0.00147 AC: 8 AN: 5430

European-Non Finnish (NFE) AF: 0.0000965 AC: 104 AN: 1077194

Other (OTH) AF: 0.00135 AC: 78 AN: 57884

GnomAD4 genome AF: 0.00506 AC: 770 AN: 152314 Hom.: 5 Cov.: 32 AF XY: 0.00485 AC XY: 361 AN XY: 74472

African (AFR) AF: 0.0173 AC: 719 AN: 41558

American (AMR) AF: 0.00183 AC: 28 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5186

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4830

European-Finnish (FIN) AF: 0.0000941 AC: 1 AN: 10622

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000221 AC: 15 AN: 68020

Other (OTH) AF: 0.00237 AC: 5 AN: 2114

Alfa AF: 0.00204 Hom.: 1

Bravo AF: 0.00578

Asia WGS AF: 0.000577 AC: 2 AN: 3478

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	1	SLC28A1-related disorder (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.9
DANN	Benign	0.68
PhyloP100		-0.25
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000041
dbscSNV1_RF	Benign	0.0
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: rs8187742; hg19: chr15-85431993; COSMIC: COSV99723541;