ENST00000435284.3:n.990-552G>C

Variant names:

• chr9-134544368-G-C
• rs3132307
• ENST00000435284.3:n.990-552G>C

Variant summary

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

The ENST00000435284.3(ENSG00000228877):​n.990-552G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,154 control chromosomes in the GnomAD database, including 6,983 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 (6983 hom., cov: 33)
• Consequence: ENSG00000228877 ENST00000435284.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275

Genes affected

ENSG00000228877 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100506532	NR_188441.1	n.184-552G>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228877	ENST00000435284.3	n.990-552G>C		intron_variant	Intron 1 of 1	3
ENSG00000228877	ENST00000745249.1	n.1012-552G>C		intron_variant	Intron 7 of 7
ENSG00000228877	ENST00000745250.1	n.271-552G>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45144 AN: 152036 Hom.: 6981 Cov.: 33

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.297 AC: 45165 AN: 152154 Hom.: 6983 Cov.: 33 AF XY: 0.296 AC XY: 22053 AN XY: 74390

African (AFR) AF: 0.237 AC: 9852 AN: 41530

American (AMR) AF: 0.295 AC: 4512 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1166 AN: 3472

East Asian (EAS) AF: 0.379 AC: 1956 AN: 5160

South Asian (SAS) AF: 0.507 AC: 2444 AN: 4822

European-Finnish (FIN) AF: 0.239 AC: 2525 AN: 10584

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.318 AC: 21631 AN: 67984

Other (OTH) AF: 0.323 AC: 681 AN: 2110

Alfa AF: 0.297 Hom.: 828

Bravo AF: 0.292

Asia WGS AF: 0.420 AC: 1458 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	3.0
DANN	Benign	0.35
PhyloP100		0.28

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: rs3132307; hg19: chr9-137436214;