rs3118515

Variant names:

• chr9-134544468-G-A
• rs3118515
• ENST00000435284.3:n.990-452G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-134544468-G-A
• chr9-134544468-G-C
• chr9-134544468-G-T

Variant summary

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

The ENST00000435284.3(ENSG00000228877):​n.990-452G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 152,160 control chromosomes in the GnomAD database, including 7,277 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 0.30 (7277 hom., cov: 33)
• Consequence: ENSG00000228877 ENST00000435284.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.294
• Publications: 15 publications found

Genes affected

ENSG00000228877 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100506532	NR_188441.1	n.184-452G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228877	ENST00000435284.3	n.990-452G>A		intron_variant	Intron 1 of 1	3
ENSG00000228877	ENST00000745249.1	n.1012-452G>A		intron_variant	Intron 7 of 7
ENSG00000228877	ENST00000745250.1	n.271-452G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46329 AN: 152042 Hom.: 7271 Cov.: 33

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.305 AC: 46370 AN: 152160 Hom.: 7277 Cov.: 33 AF XY: 0.304 AC XY: 22626 AN XY: 74390

African (AFR) AF: 0.269 AC: 11168 AN: 41526

American (AMR) AF: 0.296 AC: 4528 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1164 AN: 3468

East Asian (EAS) AF: 0.402 AC: 2074 AN: 5162

South Asian (SAS) AF: 0.497 AC: 2397 AN: 4824

European-Finnish (FIN) AF: 0.238 AC: 2526 AN: 10594

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.315 AC: 21415 AN: 67978

Other (OTH) AF: 0.332 AC: 702 AN: 2112

Alfa AF: 0.306 Hom.: 20267

Bravo AF: 0.302

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.61
DANN	Benign	0.70
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs3118515; hg19: chr9-137436314;