rs1536478

Positions:

• chr9-134540402-G-A
• chr9-134540402-G-C

Variant summary

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

The ENST00000435284.2(ENSG00000228877):​n.104-4518G>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 ENST00000435284.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.44

Genes affected

ENSG00000228877 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100506532	NR_188441.1	n.184-4518G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000228877	ENST00000435284.2	n.104-4518G>A		intron_variant		3

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

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.370

Alfa AF: 0.331 Hom.: 3636

Bravo AF: 0.369

Asia WGS AF: 0.305 AC: 1063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1536478; hg19: chr9-137432248;