rs884329

Variant names:

• chr4-105002314-T-C
• rs884329
• ENST00000506148.6:n.278+32967T>C

Variant summary

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

The ENST00000506148.6(ENSG00000248373):​n.278+32967T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 151,960 control chromosomes in the GnomAD database, including 10,350 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 0.34 (10350 hom., cov: 30)
• Consequence: ENSG00000248373 ENST00000506148.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 2 publications found

Genes affected

ENSG00000248373 (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 (NFE) allele frequency at 95% confidence interval = 0.443 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
ENSG00000248373	ENST00000506148.6	n.278+32967T>C		intron_variant	Intron 2 of 4	5
ENSG00000248373	ENST00000506386.1	n.71+28532T>C		intron_variant	Intron 1 of 3	3
ENSG00000248373	ENST00000671069.2	n.636+32967T>C		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51370 AN: 151842 Hom.: 10349 Cov.: 30

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.0797

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.338 AC: 51370 AN: 151960 Hom.: 10350 Cov.: 30 AF XY: 0.339 AC XY: 25154 AN XY: 74270

African (AFR) AF: 0.134 AC: 5540 AN: 41486

American (AMR) AF: 0.343 AC: 5243 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.547 AC: 1898 AN: 3470

East Asian (EAS) AF: 0.0799 AC: 413 AN: 5170

South Asian (SAS) AF: 0.416 AC: 2006 AN: 4820

European-Finnish (FIN) AF: 0.430 AC: 4527 AN: 10532

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.448 AC: 30387 AN: 67902

Other (OTH) AF: 0.385 AC: 812 AN: 2108

Alfa AF: 0.359 Hom.: 2211

Bravo AF: 0.316

Asia WGS AF: 0.258 AC: 896 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.5
DANN	Benign	0.84
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs884329; hg19: chr4-105923471;