9-23546463-G-T

Variant names:

• chr9-23546463-G-T
• rs7028484
• ENST00000640307.1:n.2512+4279C>A

Variant summary

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

The ENST00000640307.1(ENSG00000283982):​n.2512+4279C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 151,940 control chromosomes in the GnomAD database, including 8,553 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 0.31 (8553 hom., cov: 31)
• Consequence: ENSG00000283982 ENST00000640307.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700
• Publications: 3 publications found

Genes affected

ENSG00000283982 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000640307.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC101929563	NR_121602.1		n.2524+4279C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283982	ENST00000640307.1	TSL:1	n.2512+4279C>A		intron	N/A
	ENSG00000283982	ENST00000785123.1		n.239-5739C>A		intron	N/A
	ENSG00000283982	ENST00000785124.1		n.260+4279C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47752 AN: 151820 Hom.: 8531 Cov.: 31

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.315 AC: 47824 AN: 151940 Hom.: 8553 Cov.: 31 AF XY: 0.311 AC XY: 23115 AN XY: 74260

African (AFR) AF: 0.491 AC: 20328 AN: 41440

American (AMR) AF: 0.275 AC: 4202 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1151 AN: 3468

East Asian (EAS) AF: 0.185 AC: 954 AN: 5144

South Asian (SAS) AF: 0.264 AC: 1268 AN: 4796

European-Finnish (FIN) AF: 0.236 AC: 2490 AN: 10566

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16550 AN: 67936

Other (OTH) AF: 0.286 AC: 603 AN: 2106

Alfa AF: 0.269 Hom.: 13705

Bravo AF: 0.326

Asia WGS AF: 0.241 AC: 843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.79
DANN	Benign	0.25
PhyloP100		0.070

Splicing

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

Other links and lift over

dbSNP: rs7028484; hg19: chr9-23546461;