chr11-35421061-T-C

Variant names:

• chr11-35421061-T-C
• rs1923295
• ENST00000844059.1:n.146+1954T>C

Variant summary

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

The ENST00000844059.1(SLC1A2-AS2):​n.146+1954T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 152,000 control chromosomes in the GnomAD database, including 21,794 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 0.53 (21786 hom., cov: 31)
  • Exomes 𝑓: 0.39 (8 hom.)
• Consequence: SLC1A2-AS2 ENST00000844059.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.495
• Publications: 4 publications found

Genes affected

SLC1A2-AS2 (HGNC:40535): (SLC1A2 antisense RNA 2)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000844059.1. 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
	SLC1A2-AS2	NR_186310.1		n.*59T>C		downstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC1A2-AS2	ENST00000844059.1		n.146+1954T>C		intron	N/A
	SLC1A2-AS2	ENST00000844060.1		n.146+1954T>C		intron	N/A
	SLC1A2-AS2	ENST00000534165.1	TSL:3	n.*59T>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80101 AN: 151802 Hom.: 21758 Cov.: 31

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.519

GnomAD4 exome AF: 0.388 AC: 31 AN: 80 Hom.: 8 AF XY: 0.352 AC XY: 19 AN XY: 54

African (AFR) AF: 1.00 AC: 2 AN: 2

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: 0.833 AC: 5 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.329 AC: 23 AN: 70

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.528 AC: 80182 AN: 151920 Hom.: 21786 Cov.: 31 AF XY: 0.530 AC XY: 39354 AN XY: 74260

African (AFR) AF: 0.638 AC: 26440 AN: 41410

American (AMR) AF: 0.564 AC: 8614 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1953 AN: 3468

East Asian (EAS) AF: 0.547 AC: 2821 AN: 5158

South Asian (SAS) AF: 0.443 AC: 2132 AN: 4814

European-Finnish (FIN) AF: 0.525 AC: 5547 AN: 10556

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.458 AC: 31090 AN: 67928

Other (OTH) AF: 0.512 AC: 1078 AN: 2104

Alfa AF: 0.490 Hom.: 34529

Bravo AF: 0.538

Asia WGS AF: 0.467 AC: 1625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.6
DANN	Benign	0.78
PhyloP100		-0.49
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1923295; hg19: chr11-35442608;