rs11652536

Variant names:

• chr17-35891043-C-T
• rs11652536
• ENST00000788667.1:n.313G>A

Variant summary

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

The ENST00000788667.1(ENSG00000293240):​n.313G>A 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 0.135 in 151,892 control chromosomes in the GnomAD database, including 1,528 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 0.13 (1528 hom., cov: 30)
• Consequence: ENSG00000293240 ENST00000788667.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 1 publications found

Genes affected

ENSG00000293240 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.205 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
ENSG00000293240	ENST00000788667.1	n.313G>A		non_coding_transcript_exon_variant	Exon 2 of 3
ENSG00000293240	ENST00000788670.1	n.258G>A		non_coding_transcript_exon_variant	Exon 2 of 3
ENSG00000270240	ENST00000788495.1	n.411+6508C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20401 AN: 151776 Hom.: 1519 Cov.: 30

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.135 AC: 20436 AN: 151892 Hom.: 1528 Cov.: 30 AF XY: 0.134 AC XY: 9966 AN XY: 74230

African (AFR) AF: 0.174 AC: 7220 AN: 41394

American (AMR) AF: 0.167 AC: 2553 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 513 AN: 3464

East Asian (EAS) AF: 0.216 AC: 1112 AN: 5150

South Asian (SAS) AF: 0.113 AC: 541 AN: 4802

European-Finnish (FIN) AF: 0.112 AC: 1180 AN: 10566

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.101 AC: 6860 AN: 67940

Other (OTH) AF: 0.136 AC: 287 AN: 2114

Alfa AF: 0.114 Hom.: 171

Bravo AF: 0.144

Asia WGS AF: 0.152 AC: 528 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.093
DANN	Benign	0.47
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs11652536; hg19: chr17-34218047;