rs4836643

Positions:

• chr9-129197852-G-A
• chr9-129197852-G-C
• chr9-129197852-G-T

Variant summary

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

The ENST00000674627.1(IER5L-AS1):​n.813-11017G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 152,040 control chromosomes in the GnomAD database, including 15,321 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 0.42 (15321 hom., cov: 31)
• Consequence: IER5L-AS1 ENST00000674627.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.190

Genes affected

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

LOC105376289 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376289	XR_007061813.1	n.1415-11017G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IER5L-AS1	ENST00000674627.1	n.813-11017G>A		intron_variant, non_coding_transcript_variant
IER5L-AS1	ENST00000372490.4	n.368-11017G>A		intron_variant, non_coding_transcript_variant		2
IER5L-AS1	ENST00000675308.1	n.813-11017G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63328 AN: 151922 Hom.: 15318 Cov.: 31

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.417 AC: 63332 AN: 152040 Hom.: 15321 Cov.: 31 AF XY: 0.417 AC XY: 31002 AN XY: 74300

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.464

Gnomad4 ASJ AF: 0.604

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.423

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.483

Alfa AF: 0.516 Hom.: 26891

Bravo AF: 0.408

Asia WGS AF: 0.562 AC: 1954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.0
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4836643; hg19: chr9-131960131;