9-84574740-T-G

Variant names:

• chr9-84574740-T-G
• rs10868204
• ENST00000650453.1:n.979-8457T>G

Variant summary

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

The ENST00000650453.1(ENSG00000285987):​n.979-8457T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 151,970 control chromosomes in the GnomAD database, including 8,372 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 0.33 (8372 hom., cov: 32)
• Consequence: ENSG00000285987 ENST00000650453.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 1 publications found

Genes affected

ENSG00000285987 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650453.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285987	ENST00000650453.1		n.979-8457T>G		intron	N/A
	ENSG00000285987	ENST00000728338.1		n.1046-8457T>G		intron	N/A
	ENSG00000285987	ENST00000728339.1		n.784-4031T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.329 AC: 49997 AN: 151852 Hom.: 8352 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.329 AC: 50073 AN: 151970 Hom.: 8372 Cov.: 32 AF XY: 0.332 AC XY: 24669 AN XY: 74294

African (AFR) AF: 0.335 AC: 13861 AN: 41434

American (AMR) AF: 0.377 AC: 5749 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1105 AN: 3468

East Asian (EAS) AF: 0.410 AC: 2114 AN: 5158

South Asian (SAS) AF: 0.385 AC: 1853 AN: 4808

European-Finnish (FIN) AF: 0.308 AC: 3260 AN: 10576

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 21013 AN: 67944

Other (OTH) AF: 0.347 AC: 732 AN: 2110

Alfa AF: 0.278 Hom.: 2020

Bravo AF: 0.334

Asia WGS AF: 0.454 AC: 1574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.48
DANN	Benign	0.62
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10868204; hg19: chr9-87189655;