5-143750479-G-C

Variant names:

• chr5-143750479-G-C
• rs325229
• ENST00000503323.1:n.379+77782G>C

Variant summary

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

The ENST00000503323.1(ENSG00000249881):​n.379+77782G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 151,834 control chromosomes in the GnomAD database, including 14,111 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 0.43 (14111 hom., cov: 31)
• Consequence: ENSG00000249881 ENST00000503323.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 2 publications found

Genes affected

ENSG00000249881 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.542 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
ENSG00000249881	ENST00000503323.1	n.379+77782G>C		intron_variant	Intron 4 of 4	3
ENSG00000293852	ENST00000719486.1	n.439-10711C>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64627 AN: 151716 Hom.: 14094 Cov.: 31

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.426 AC: 64685 AN: 151834 Hom.: 14111 Cov.: 31 AF XY: 0.426 AC XY: 31576 AN XY: 74190

African (AFR) AF: 0.510 AC: 21099 AN: 41392

American (AMR) AF: 0.440 AC: 6717 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1482 AN: 3472

East Asian (EAS) AF: 0.559 AC: 2876 AN: 5144

South Asian (SAS) AF: 0.399 AC: 1917 AN: 4804

European-Finnish (FIN) AF: 0.383 AC: 4032 AN: 10518

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.370 AC: 25098 AN: 67924

Other (OTH) AF: 0.407 AC: 857 AN: 2108

Alfa AF: 0.236 Hom.: 485

Bravo AF: 0.439

Asia WGS AF: 0.452 AC: 1573 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.23
DANN	Benign	0.27
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs325229; hg19: chr5-143130044;