rs11582424

Variant names:

• chr1-154391509-A-C
• rs11582424
• ENST00000745818.1:n.589T>G

Your query was ambiguous. Multiple possible variants found:

• chr1-154391509-A-C
• chr1-154391509-A-G

Variant summary

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

The ENST00000745818.1(ENSG00000297143):​n.589T>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 0.284 in 151,972 control chromosomes in the GnomAD database, including 6,247 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 0.28 (6247 hom., cov: 31)
• Consequence: ENSG00000297143 ENST00000745818.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 7 publications found

Genes affected

ENSG00000297143 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000745818.1. 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
	ENSG00000297143	ENST00000745818.1		n.589T>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000297143	ENST00000745819.1		n.427T>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000297143	ENST00000745817.1		n.212-8131T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43209 AN: 151854 Hom.: 6243 Cov.: 31

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.284 AC: 43235 AN: 151972 Hom.: 6247 Cov.: 31 AF XY: 0.283 AC XY: 21019 AN XY: 74270

African (AFR) AF: 0.284 AC: 11771 AN: 41462

American (AMR) AF: 0.305 AC: 4649 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 744 AN: 3462

East Asian (EAS) AF: 0.268 AC: 1381 AN: 5158

South Asian (SAS) AF: 0.248 AC: 1196 AN: 4822

European-Finnish (FIN) AF: 0.304 AC: 3214 AN: 10564

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19363 AN: 67954

Other (OTH) AF: 0.275 AC: 580 AN: 2106

Alfa AF: 0.282 Hom.: 19092

Bravo AF: 0.286

Asia WGS AF: 0.232 AC: 809 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.2
DANN	Benign	0.17
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs11582424; hg19: chr1-154363985;