rs600231

Variant names:

• chr11-65493175-A-G
• rs600231
• ENST00000702719.1:n.-117T>C

Your query was ambiguous. Multiple possible variants found:

• chr11-65493175-A-G
• chr11-65493175-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000702719.1(ENSG00000290061):​n.-117T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 152,048 control chromosomes in the GnomAD database, including 16,478 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 0.42 (16478 hom., cov: 31)
• Consequence: ENSG00000290061 ENST00000702719.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390

Genes affected

ENSG00000290061 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.689 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
ENSG00000290061	ENST00000702719.1	n.-117T>C		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64457 AN: 151930 Hom.: 16445 Cov.: 31

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.424 AC: 64544 AN: 152048 Hom.: 16478 Cov.: 31 AF XY: 0.418 AC XY: 31068 AN XY: 74304

Gnomad4 AFR AF: 0.696

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.380

Alfa AF: 0.319 Hom.: 16382

Bravo AF: 0.466

Asia WGS AF: 0.405 AC: 1410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.5
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs600231; hg19: chr11-65260646;