rs732165

Variant names:

• chr15-35061996-G-A
• rs732165
• ENST00000692204.2:n.71C>T

Variant summary

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

The ENST00000692204.2(ENSG00000289289):​n.71C>T 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 0.292 in 152,076 control chromosomes in the GnomAD database, including 7,814 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 0.29 (7814 hom., cov: 32)
• Consequence: ENSG00000289289 ENST00000692204.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200

Genes affected

ENSG00000289289 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.394 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
ENSG00000289289	ENST00000692204.2	n.71C>T		non_coding_transcript_exon_variant	Exon 2 of 3

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44346 AN: 151958 Hom.: 7816 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.0853

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.292 AC: 44332 AN: 152076 Hom.: 7814 Cov.: 32 AF XY: 0.291 AC XY: 21612 AN XY: 74320

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.0845

Gnomad4 SAS AF: 0.261

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.331

Alfa AF: 0.382 Hom.: 22852

Bravo AF: 0.275

Asia WGS AF: 0.175 AC: 609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs732165; hg19: chr15-35354197;