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

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376289	XR_007061813.1	n.1415-11017G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000235007	ENST00000674648.1	c.109-11017G>A		intron_variant	Intron 2 of 2			ENSP00000502744.1

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 v4.3

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

Publications

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Other links and lift over

dbSNP: rs4836643; hg19: chr9-131960131;