11-2889391-T-C

Variant names:

• chr11-2889391-T-C
• rs10832869
• ENST00000455942.5:n.483-756A>G

Variant summary

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

The ENST00000455942.5(SLC22A18AS):​n.483-756A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 152,028 control chromosomes in the GnomAD database, including 9,925 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 0.35 (9922 hom., cov: 34)
  • Exomes 𝑓: 0.36 (3 hom.)
• Consequence: SLC22A18AS ENST00000455942.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.791
• Publications: 7 publications found

Genes affected

SLC22A18AS (HGNC:10965): (SLC22A18 antisense RNA)

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 (EAS) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000455942.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC67A1-AS	NR_169304.1		n.639-756A>G		intron	N/A
	SLC67A1-AS	NR_169305.1		n.244-756A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A18AS	ENST00000455942.5	TSL:1	n.483-756A>G		intron	N/A
	SLC22A18AS	ENST00000625099.4	TSL:1	n.639-756A>G		intron	N/A
	SLC22A18AS	ENST00000526203.2	TSL:3	n.175A>G		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53141 AN: 151870 Hom.: 9917 Cov.: 34

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.400

GnomAD4 exome AF: 0.357 AC: 15 AN: 42 Hom.: 3 Cov.: 0 AF XY: 0.433 AC XY: 13 AN XY: 30

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.167 AC: 1 AN: 6

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.382 AC: 13 AN: 34

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.350 AC: 53167 AN: 151986 Hom.: 9922 Cov.: 34 AF XY: 0.352 AC XY: 26124 AN XY: 74300

African (AFR) AF: 0.351 AC: 14507 AN: 41362

American (AMR) AF: 0.394 AC: 6026 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1855 AN: 3472

East Asian (EAS) AF: 0.720 AC: 3715 AN: 5162

South Asian (SAS) AF: 0.409 AC: 1975 AN: 4824

European-Finnish (FIN) AF: 0.250 AC: 2651 AN: 10598

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.311 AC: 21143 AN: 67968

Other (OTH) AF: 0.403 AC: 849 AN: 2106

Alfa AF: 0.334 Hom.: 15222

Bravo AF: 0.366

Asia WGS AF: 0.539 AC: 1873 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	2.1
DANN	Benign	0.56
PhyloP100		-0.79
PromoterAI		0.010	Neutral
Mutation Taster		=297/3	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: rs10832869; hg19: chr11-2910621;