rs4836643

Variant names:

• chr9-129197852-G-A
• rs4836643
• ENST00000674648.1:c.109-11017G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000674648.1(ENSG00000235007):​c.109-11017G>A variant causes a intron 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: ENSG00000235007 ENST00000674648.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.190
• 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000674648.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000235007	ENST00000674648.1		c.109-11017G>A		intron	N/A	ENSP00000502744.1
	IER5L-AS1	ENST00000372490.4	TSL:2	n.368-11017G>A		intron	N/A
	ENSG00000235007	ENST00000674559.1		n.109-11017G>A		intron	N/A	ENSP00000502494.1

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

African (AFR) AF: 0.154 AC: 6400 AN: 41496

American (AMR) AF: 0.464 AC: 7084 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 2093 AN: 3468

East Asian (EAS) AF: 0.673 AC: 3465 AN: 5148

South Asian (SAS) AF: 0.559 AC: 2691 AN: 4818

European-Finnish (FIN) AF: 0.423 AC: 4464 AN: 10550

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.524 AC: 35591 AN: 67968

Other (OTH) AF: 0.483 AC: 1018 AN: 2108

Alfa AF: 0.481 Hom.: 35816

Bravo AF: 0.408

Asia WGS AF: 0.562 AC: 1954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.0
DANN	Benign	0.71
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs4836643; hg19: chr9-131960131;