chr3-30134572-T-C

Variant names:

• chr3-30134572-T-C
• rs9332449
• ENST00000752605.1:n.79+9254T>C

Variant summary

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

The ENST00000752605.1(ENSG00000298038):​n.79+9254T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 152,056 control chromosomes in the GnomAD database, including 6,359 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 0.27 (6359 hom., cov: 32)
• Consequence: ENSG00000298038 ENST00000752605.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367
• Publications: 2 publications found

Genes affected

ENSG00000298038 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298038	ENST00000752605.1	n.79+9254T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41675 AN: 151938 Hom.: 6360 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.274 AC: 41678 AN: 152056 Hom.: 6359 Cov.: 32 AF XY: 0.276 AC XY: 20485 AN XY: 74322

African (AFR) AF: 0.137 AC: 5677 AN: 41512

American (AMR) AF: 0.268 AC: 4087 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 957 AN: 3470

East Asian (EAS) AF: 0.379 AC: 1952 AN: 5144

South Asian (SAS) AF: 0.288 AC: 1390 AN: 4820

European-Finnish (FIN) AF: 0.366 AC: 3869 AN: 10564

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22818 AN: 67974

Other (OTH) AF: 0.274 AC: 579 AN: 2110

Alfa AF: 0.311 Hom.: 1609

Bravo AF: 0.259

Asia WGS AF: 0.295 AC: 1027 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.67
DANN	Benign	0.72
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs9332449; hg19: chr3-30176063;