chr15-35061996-G-A

Variant names:

• chr15-35061996-G-A
• rs732165
• ENST00000692204.3:n.71C>T

Variant summary

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

The ENST00000692204.3(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 ENST00000692204.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200
• Publications: 7 publications found

Genes affected

ENSG00000289289 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000692204.3. 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
	ENSG00000289289	ENST00000692204.3		n.71C>T		non_coding_transcript_exon	Exon 2 of 3
	ENSG00000289289	ENST00000763069.1		n.72C>T		non_coding_transcript_exon	Exon 2 of 3
	ENSG00000289289	ENST00000763070.1		n.68C>T		non_coding_transcript_exon	Exon 2 of 4

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

African (AFR) AF: 0.102 AC: 4249 AN: 41502

American (AMR) AF: 0.291 AC: 4451 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1424 AN: 3470

East Asian (EAS) AF: 0.0845 AC: 438 AN: 5182

South Asian (SAS) AF: 0.261 AC: 1257 AN: 4818

European-Finnish (FIN) AF: 0.405 AC: 4277 AN: 10548

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 27053 AN: 67960

Other (OTH) AF: 0.331 AC: 699 AN: 2112

Alfa AF: 0.374 Hom.: 32288

Bravo AF: 0.275

Asia WGS AF: 0.175 AC: 609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.59
PhyloP100		-0.020

Splicing

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

Other links and lift over

dbSNP: rs732165; hg19: chr15-35354197;