9-86615864-C-T

Variant names:

• chr9-86615864-C-T
• rs9696070
• ENST00000739587.1:n.167-16273C>T

Variant summary

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

The ENST00000739587.1(ENSG00000232211):​n.167-16273C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 151,930 control chromosomes in the GnomAD database, including 13,290 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 (13290 hom., cov: 32)
• Consequence: ENSG00000232211 ENST00000739587.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 3 publications found

Genes affected

ENSG00000232211 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000739587.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000232211	ENST00000739587.1		n.167-16273C>T		intron	N/A
	ENSG00000232211	ENST00000739588.1		n.112+40C>T		intron	N/A
	ENSG00000232211	ENST00000739589.1		n.98+2896C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63310 AN: 151812 Hom.: 13279 Cov.: 32

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.378

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.417 AC: 63366 AN: 151930 Hom.: 13290 Cov.: 32 AF XY: 0.419 AC XY: 31083 AN XY: 74258

African (AFR) AF: 0.451 AC: 18681 AN: 41444

American (AMR) AF: 0.418 AC: 6379 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1537 AN: 3468

East Asian (EAS) AF: 0.434 AC: 2240 AN: 5156

South Asian (SAS) AF: 0.460 AC: 2212 AN: 4810

European-Finnish (FIN) AF: 0.381 AC: 4015 AN: 10528

Middle Eastern (MID) AF: 0.383 AC: 111 AN: 290

European-Non Finnish (NFE) AF: 0.395 AC: 26846 AN: 67950

Other (OTH) AF: 0.441 AC: 930 AN: 2108

Alfa AF: 0.401 Hom.: 55138

Bravo AF: 0.417

Asia WGS AF: 0.459 AC: 1598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.82
DANN	Benign	0.67
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs9696070; hg19: chr9-89230779;