chr9-111163254-T-C

Variant names:

• chr9-111163254-T-C
• rs7023923
• ENST00000426204.1:n.371-23635A>G

Variant summary

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

The ENST00000426204.1(ENSG00000227531):​n.371-23635A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 151,860 control chromosomes in the GnomAD database, including 19,413 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 0.50 (19413 hom., cov: 32)
• Consequence: ENSG00000227531 ENST00000426204.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.806
• Publications: 10 publications found

Genes affected

ENSG00000227531 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000426204.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000227531	ENST00000426204.1	TSL:3	n.371-23635A>G		intron	N/A
	ENSG00000308512	ENST00000834703.1		n.-55T>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76053 AN: 151742 Hom.: 19385 Cov.: 32

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.501 AC: 76138 AN: 151860 Hom.: 19413 Cov.: 32 AF XY: 0.495 AC XY: 36757 AN XY: 74216

African (AFR) AF: 0.564 AC: 23358 AN: 41400

American (AMR) AF: 0.412 AC: 6282 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1828 AN: 3472

East Asian (EAS) AF: 0.226 AC: 1164 AN: 5160

South Asian (SAS) AF: 0.463 AC: 2225 AN: 4806

European-Finnish (FIN) AF: 0.468 AC: 4939 AN: 10562

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.511 AC: 34693 AN: 67900

Other (OTH) AF: 0.495 AC: 1044 AN: 2108

Alfa AF: 0.502 Hom.: 2147

Bravo AF: 0.496

Asia WGS AF: 0.387 AC: 1346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.45
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs7023923; hg19: chr9-113925534;