rs600231

Variant names:

• chr11-65493175-A-G
• rs600231
• ENST00000702719.2:n.795T>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000702719.2(ENSG00000290061):​n.795T>C 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 0.424 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 ENST00000702719.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390
• Publications: 30 publications found

Genes affected

ENSG00000290061 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000702719.2. 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
	ENSG00000290061	ENST00000702719.2		n.795T>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000300048	ENST00000768429.1		n.54A>G		non_coding_transcript_exon	Exon 1 of 1

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

African (AFR) AF: 0.696 AC: 28837 AN: 41426

American (AMR) AF: 0.484 AC: 7385 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 951 AN: 3472

East Asian (EAS) AF: 0.424 AC: 2194 AN: 5176

South Asian (SAS) AF: 0.379 AC: 1826 AN: 4822

European-Finnish (FIN) AF: 0.180 AC: 1907 AN: 10600

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20194 AN: 67976

Other (OTH) AF: 0.380 AC: 802 AN: 2112

Alfa AF: 0.348 Hom.: 34024

Bravo AF: 0.466

Asia WGS AF: 0.405 AC: 1410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.5
DANN	Benign	0.48
PhyloP100		-0.039

Splicing

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

Other links and lift over

dbSNP: rs600231; hg19: chr11-65260646;