9-85506654-G-T

Variant names:

• chr9-85506654-G-T
• rs1014690
• ENST00000812125.1:n.138+9676C>A

Variant summary

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

The ENST00000812125.1(ENSG00000285634):​n.138+9676C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,156 control chromosomes in the GnomAD database, including 1,774 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 (1774 hom., cov: 33)
• Consequence: ENSG00000285634 ENST00000812125.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22
• Publications: 0 publications found

Genes affected

ENSG00000285634 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812125.1. 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
	ENSG00000285634	ENST00000812125.1		n.138+9676C>A		intron	N/A
	ENSG00000285634	ENST00000812126.1		n.153+9676C>A		intron	N/A
	ENSG00000285634	ENST00000812127.1		n.123+4384C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20275 AN: 152038 Hom.: 1757 Cov.: 33

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0841

Gnomad EAS AF: 0.0512

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.0508

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.0912

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.134 AC: 20327 AN: 152156 Hom.: 1774 Cov.: 33 AF XY: 0.133 AC XY: 9888 AN XY: 74386

African (AFR) AF: 0.238 AC: 9864 AN: 41490

American (AMR) AF: 0.114 AC: 1747 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0841 AC: 292 AN: 3470

East Asian (EAS) AF: 0.0512 AC: 265 AN: 5180

South Asian (SAS) AF: 0.204 AC: 984 AN: 4816

European-Finnish (FIN) AF: 0.0508 AC: 538 AN: 10590

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.0911 AC: 6197 AN: 68008

Other (OTH) AF: 0.149 AC: 315 AN: 2112

Alfa AF: 0.0715 Hom.: 153

Bravo AF: 0.142

Asia WGS AF: 0.171 AC: 592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.8
DANN	Benign	0.44
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs1014690; hg19: chr9-88121569; COSMIC: COSV60371601;