11-2889391-T-C

Position:

• chr11-2889391-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_169305.1(SLC22A18AS):​n.244-756A>G variant causes a intron, non coding transcript 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 NR_169305.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.791

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC22A18AS	NR_169305.1	n.244-756A>G		intron_variant, non_coding_transcript_variant
SLC22A18AS	NR_169304.1	n.639-756A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC22A18AS	ENST00000455942.4	n.482-756A>G		intron_variant, non_coding_transcript_variant		1
SLC22A18AS	ENST00000625099.4	n.639-756A>G		intron_variant, non_coding_transcript_variant		1
SLC22A18AS	ENST00000702349.1	n.356-756A>G		intron_variant, non_coding_transcript_variant
SLC22A18AS	ENST00000526203.1	n.40A>G		non_coding_transcript_exon_variant	1/2	3

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

Gnomad4 FIN exome AF: 0.167

Gnomad4 NFE exome AF: 0.382

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

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.720

Gnomad4 SAS AF: 0.409

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.403

Alfa AF: 0.331 Hom.: 11882

Bravo AF: 0.366

Asia WGS AF: 0.539 AC: 1873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.1
DANN	Benign	0.56

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

Publications

LitVar

Other links and lift over

dbSNP: rs10832869; hg19: chr11-2910621;