ENST00000844370.1:n.142T>G

Variant names:

• chr11-35247407-A-C
• rs10488813
• ENST00000844370.1:n.142T>G

Variant summary

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

The ENST00000844370.1(ENSG00000309853):​n.142T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,174 control chromosomes in the GnomAD database, including 1,138 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 0.12 (1138 hom., cov: 33)
• Consequence: ENSG00000309853 ENST00000844370.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 1 publications found

Genes affected

ENSG00000309853 (HGNC:):

SLC1A2-AS1 (HGNC:40534): (SLC1A2 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309853	ENST00000844370.1	n.142T>G		non_coding_transcript_exon_variant	Exon 1 of 1
SLC1A2-AS1	ENST00000844195.1	n.426+9013A>C		intron_variant	Intron 1 of 2
SLC1A2-AS1	ENST00000844196.1	n.328+9013A>C		intron_variant	Intron 1 of 1
SLC1A2-AS1	ENST00000844197.1	n.425+9013A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17679 AN: 152056 Hom.: 1122 Cov.: 33

Gnomad AFR AF: 0.0696

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.0686

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.117 AC: 17729 AN: 152174 Hom.: 1138 Cov.: 33 AF XY: 0.118 AC XY: 8748 AN XY: 74376

African (AFR) AF: 0.0698 AC: 2901 AN: 41534

American (AMR) AF: 0.183 AC: 2796 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 430 AN: 3470

East Asian (EAS) AF: 0.153 AC: 789 AN: 5166

South Asian (SAS) AF: 0.0682 AC: 328 AN: 4808

European-Finnish (FIN) AF: 0.133 AC: 1405 AN: 10596

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8701 AN: 67990

Other (OTH) AF: 0.135 AC: 285 AN: 2108

Alfa AF: 0.110 Hom.: 115

Bravo AF: 0.119

Asia WGS AF: 0.151 AC: 525 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.75
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10488813; hg19: chr11-35268954;