rs1075650

chr9-129176634-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_203434.3(IER5L):c.*204A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 661,754 control chromosomes in the GnomAD database, including 26,158 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 0.25 (4911 hom., cov: 32)
  • Exomes 𝑓: 0.28 (21247 hom.)
• Consequence: IER5L NM_203434.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.94

Genes affected

IER5L (HGNC:23679): (immediate early response 5 like)

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IER5L	NM_203434.3	c.*204A>G		3_prime_UTR_variant	1/1	ENST00000372491.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IER5L	ENST00000372491.4	c.*204A>G		3_prime_UTR_variant	1/1		NM_203434.3	P1
IER5L-AS1	ENST00000674627.1	n.309T>C		non_coding_transcript_exon_variant	1/6

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37383 AN: 151910 Hom.: 4908 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.292

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.257

GnomAD4 exome AF: 0.282 AC: 143590 AN: 509732 Hom.: 21247 Cov.: 8 AF XY: 0.281 AC XY: 71566 AN XY: 254698

Gnomad4 AFR exome AF: 0.157

Gnomad4 AMR exome AF: 0.191

Gnomad4 ASJ exome AF: 0.241

Gnomad4 EAS exome AF: 0.114

Gnomad4 SAS exome AF: 0.242

Gnomad4 FIN exome AF: 0.240

Gnomad4 NFE exome AF: 0.304

Gnomad4 OTH exome AF: 0.278

GnomAD4 genome AF: 0.246 AC: 37403 AN: 152022 Hom.: 4911 Cov.: 32 AF XY: 0.241 AC XY: 17886 AN XY: 74324

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.256

Alfa AF: 0.290 Hom.: 8220

Bravo AF: 0.240

Asia WGS AF: 0.224 AC: 776 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
Cadd	Benign	17
Dann	Benign	0.88

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1075650; hg19: chr9-131938913;