chr11-35237860-A-C

Variant names:

• chr11-35237860-A-C
• rs7105418
• ENST00000844195.1:n.-109A>C

Variant summary

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

The ENST00000844195.1(SLC1A2-AS1):​n.-109A>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 152,032 control chromosomes in the GnomAD database, including 22,695 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 0.54 (22695 hom., cov: 32)
• Consequence: SLC1A2-AS1 ENST00000844195.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.39
• Publications: 3 publications found

Genes affected

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000844195.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC1A2-AS1	ENST00000844195.1		n.-109A>C		upstream_gene	N/A
	SLC1A2-AS1	ENST00000844196.1		n.-207A>C		upstream_gene	N/A
	SLC1A2-AS1	ENST00000844197.1		n.-110A>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.540 AC: 82015 AN: 151914 Hom.: 22679 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.540 AC: 82074 AN: 152032 Hom.: 22695 Cov.: 32 AF XY: 0.547 AC XY: 40640 AN XY: 74290

African (AFR) AF: 0.400 AC: 16574 AN: 41448

American (AMR) AF: 0.578 AC: 8832 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 2373 AN: 3468

East Asian (EAS) AF: 0.532 AC: 2749 AN: 5170

South Asian (SAS) AF: 0.615 AC: 2968 AN: 4828

European-Finnish (FIN) AF: 0.624 AC: 6579 AN: 10536

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.589 AC: 40071 AN: 67978

Other (OTH) AF: 0.547 AC: 1158 AN: 2116

Alfa AF: 0.558 Hom.: 5234

Bravo AF: 0.526

Asia WGS AF: 0.571 AC: 1982 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.074
DANN	Benign	0.66
PhyloP100		-3.4

Splicing

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

Other links and lift over

dbSNP: rs7105418; hg19: chr11-35259407;