9-82732698-G-T

Variant names:

• chr9-82732698-G-T
• rs609444
• ENST00000637606.1:n.986-47181G>T

Variant summary

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

The ENST00000637606.1(ENSG00000290551):​n.986-47181G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 152,018 control chromosomes in the GnomAD database, including 16,755 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 0.46 (16755 hom., cov: 32)
• Consequence: ENSG00000290551 ENST00000637606.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.601
• Publications: 0 publications found

Genes affected

ENSG00000290551 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000637606.1. 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
	ENSG00000290551	ENST00000637606.1	TSL:5	n.986-47181G>T		intron	N/A
	ENSG00000303186	ENST00000792612.1		n.331+9506C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69880 AN: 151900 Hom.: 16749 Cov.: 32

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.460 AC: 69931 AN: 152018 Hom.: 16755 Cov.: 32 AF XY: 0.453 AC XY: 33686 AN XY: 74292

African (AFR) AF: 0.563 AC: 23359 AN: 41468

American (AMR) AF: 0.497 AC: 7590 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1304 AN: 3472

East Asian (EAS) AF: 0.177 AC: 913 AN: 5160

South Asian (SAS) AF: 0.266 AC: 1280 AN: 4816

European-Finnish (FIN) AF: 0.449 AC: 4741 AN: 10554

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.431 AC: 29282 AN: 67978

Other (OTH) AF: 0.414 AC: 871 AN: 2104

Alfa AF: 0.435 Hom.: 38208

Bravo AF: 0.472

Asia WGS AF: 0.227 AC: 788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
DANN	Benign	0.81
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs609444; hg19: chr9-85347613;