9-129234683-C-T

Variant names:

• chr9-129234683-C-T
• rs9409314
• ENST00000674559.1:n.*231-22215C>T

Variant summary

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

The ENST00000674559.1(ENSG00000235007):​n.*231-22215C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 152,224 control chromosomes in the GnomAD database, including 22,963 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 0.51 (22963 hom., cov: 34)
• Consequence: ENSG00000235007 ENST00000674559.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.84
• Publications: 3 publications found

Genes affected

ENSG00000235007 (HGNC:):

IER5L-AS1 (HGNC:55825): (IER5L antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000235007	ENST00000674559.1	n.*231-22215C>T		intron_variant	Intron 3 of 6			ENSP00000502494.1
IER5L-AS1	ENST00000674627.1	n.1181-22215C>T		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78117 AN: 152106 Hom.: 22967 Cov.: 34

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.513 AC: 78123 AN: 152224 Hom.: 22963 Cov.: 34 AF XY: 0.513 AC XY: 38191 AN XY: 74430

African (AFR) AF: 0.215 AC: 8943 AN: 41536

American (AMR) AF: 0.547 AC: 8362 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.705 AC: 2448 AN: 3472

East Asian (EAS) AF: 0.415 AC: 2144 AN: 5170

South Asian (SAS) AF: 0.574 AC: 2769 AN: 4826

European-Finnish (FIN) AF: 0.630 AC: 6684 AN: 10610

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.660 AC: 44851 AN: 68000

Other (OTH) AF: 0.563 AC: 1188 AN: 2112

Alfa AF: 0.610 Hom.: 109478

Bravo AF: 0.492

Asia WGS AF: 0.461 AC: 1605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.0030
DANN	Benign	0.68
PhyloP100		-4.8

Splicing

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

Other links and lift over

dbSNP: rs9409314; hg19: chr9-131996962;