9-87330642-T-A

Variant names:

• chr9-87330642-T-A
• rs2378731
• ENST00000690842.2:n.743-33102A>T

Variant summary

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

The ENST00000690842.2(ENSG00000289166):​n.743-33102A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,222 control chromosomes in the GnomAD database, including 2,168 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 0.16 (2168 hom., cov: 33)
• Consequence: ENSG00000289166 ENST00000690842.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169
• Publications: 3 publications found

Genes affected

ENSG00000289166 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000690842.2. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289166	ENST00000690842.2		n.743-33102A>T		intron	N/A
	ENSG00000289166	ENST00000804132.1		n.217-33102A>T		intron	N/A
	ENSG00000289166	ENST00000804133.1		n.379-33102A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24032 AN: 152104 Hom.: 2165 Cov.: 33

Gnomad AFR AF: 0.0802

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.158 AC: 24040 AN: 152222 Hom.: 2168 Cov.: 33 AF XY: 0.160 AC XY: 11944 AN XY: 74420

African (AFR) AF: 0.0801 AC: 3329 AN: 41536

American (AMR) AF: 0.257 AC: 3935 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 799 AN: 3472

East Asian (EAS) AF: 0.232 AC: 1197 AN: 5168

South Asian (SAS) AF: 0.155 AC: 750 AN: 4828

European-Finnish (FIN) AF: 0.172 AC: 1820 AN: 10602

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11495 AN: 68010

Other (OTH) AF: 0.178 AC: 376 AN: 2116

Alfa AF: 0.163 Hom.: 298

Bravo AF: 0.162

Asia WGS AF: 0.193 AC: 668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.6
DANN	Benign	0.77
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs2378731; hg19: chr9-89945557;