rs9878448

Variant names:

• chr3-30946248-C-T
• rs9878448
• ENST00000824914.1:n.263-13881G>A

Variant summary

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

The ENST00000824914.1(ENSG00000307279):​n.263-13881G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,142 control chromosomes in the GnomAD database, including 2,792 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 0.11 (2792 hom., cov: 32)
• Consequence: ENSG00000307279 ENST00000824914.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900
• Publications: 0 publications found

Genes affected

ENSG00000307279 (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 (AFR) allele frequency at 95% confidence interval = 0.353 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
ENSG00000307279	ENST00000824914.1	n.263-13881G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17217 AN: 152024 Hom.: 2774 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0768

Gnomad ASJ AF: 0.00692

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.0456

Gnomad FIN AF: 0.00274

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.00279

Gnomad OTH AF: 0.0880

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

GnomAD4 genome AF: 0.114 AC: 17276 AN: 152142 Hom.: 2792 Cov.: 32 AF XY: 0.112 AC XY: 8351 AN XY: 74376

African (AFR) AF: 0.358 AC: 14827 AN: 41470

American (AMR) AF: 0.0768 AC: 1174 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00692 AC: 24 AN: 3470

East Asian (EAS) AF: 0.119 AC: 615 AN: 5168

South Asian (SAS) AF: 0.0456 AC: 220 AN: 4820

European-Finnish (FIN) AF: 0.00274 AC: 29 AN: 10602

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.00279 AC: 190 AN: 68004

Other (OTH) AF: 0.0871 AC: 184 AN: 2112

Alfa AF: 0.0338 Hom.: 1201

Bravo AF: 0.130

Asia WGS AF: 0.0820 AC: 284 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	0.74
DANN	Benign	0.26
PhyloP100		0.0090

Splicing

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

Other links and lift over

dbSNP: rs9878448; hg19: chr3-30987740;