11-35241591-A-G

Variant names:

• chr11-35241591-A-G
• rs4756201
• ENST00000844195.1:n.426+3197A>G

Variant summary

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

The ENST00000844195.1(SLC1A2-AS1):​n.426+3197A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.801 in 152,180 control chromosomes in the GnomAD database, including 49,675 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 0.80 (49675 hom., cov: 32)
• Consequence: SLC1A2-AS1 ENST00000844195.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 2 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.936 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC1A2-AS1	ENST00000844195.1		n.426+3197A>G		intron	N/A
	SLC1A2-AS1	ENST00000844196.1		n.328+3197A>G		intron	N/A
	SLC1A2-AS1	ENST00000844197.1		n.425+3197A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.801 AC: 121759 AN: 152062 Hom.: 49615 Cov.: 32

Gnomad AFR AF: 0.944

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.928

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.801 AC: 121882 AN: 152180 Hom.: 49675 Cov.: 32 AF XY: 0.805 AC XY: 59853 AN XY: 74382

African (AFR) AF: 0.944 AC: 39219 AN: 41558

American (AMR) AF: 0.823 AC: 12585 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.817 AC: 2836 AN: 3472

East Asian (EAS) AF: 0.928 AC: 4795 AN: 5166

South Asian (SAS) AF: 0.783 AC: 3778 AN: 4828

European-Finnish (FIN) AF: 0.717 AC: 7575 AN: 10558

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.713 AC: 48495 AN: 67982

Other (OTH) AF: 0.800 AC: 1689 AN: 2112

Alfa AF: 0.707 Hom.: 3402

Bravo AF: 0.816

Asia WGS AF: 0.855 AC: 2969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.043
DANN	Benign	0.51
PhyloP100		-1.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4756201;

hg19: chr11-35263138;