chr9-134540402-G-A

Variant names:

• chr9-134540402-G-A
• rs1536478
• ENST00000435284.3:n.990-4518G>A

Variant summary

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

The ENST00000435284.3(ENSG00000228877):​n.990-4518G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 152,092 control chromosomes in the GnomAD database, including 9,859 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 0.35 (9859 hom., cov: 32)
• Consequence: ENSG00000228877 ENST00000435284.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.44
• Publications: 11 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435284.3. 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
	LOC100506532	NR_188441.1		n.184-4518G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228877	ENST00000435284.3	TSL:3	n.990-4518G>A		intron	N/A
	ENSG00000228877	ENST00000745249.1		n.1012-4518G>A		intron	N/A
	ENSG00000228877	ENST00000745250.1		n.271-4518G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53957 AN: 151974 Hom.: 9857 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.355 AC: 53979 AN: 152092 Hom.: 9859 Cov.: 32 AF XY: 0.354 AC XY: 26316 AN XY: 74352

African (AFR) AF: 0.324 AC: 13437 AN: 41472

American (AMR) AF: 0.451 AC: 6901 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1447 AN: 3470

East Asian (EAS) AF: 0.349 AC: 1794 AN: 5146

South Asian (SAS) AF: 0.257 AC: 1243 AN: 4828

European-Finnish (FIN) AF: 0.312 AC: 3307 AN: 10594

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24555 AN: 67968

Other (OTH) AF: 0.370 AC: 783 AN: 2116

Alfa AF: 0.335 Hom.: 4163

Bravo AF: 0.369

Asia WGS AF: 0.305 AC: 1063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.044
DANN	Benign	0.43
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs1536478; hg19: chr9-137432248;