chr5-24226783-C-G

Variant names:

• chr5-24226783-C-G
• rs4443391
• ENST00000652008.2:n.254+44785G>C

Variant summary

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

The ENST00000652008.2(ENSG00000286134):​n.254+44785G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.716 in 152,018 control chromosomes in the GnomAD database, including 39,175 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 0.72 (39175 hom., cov: 31)
• Consequence: ENSG00000286134 ENST00000652008.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 4 publications found

Genes affected

ENSG00000286134 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.738 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
ENSG00000286134	ENST00000652008.2	n.254+44785G>C		intron_variant	Intron 1 of 5
ENSG00000286134	ENST00000657726.1	n.283-18475G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108707 AN: 151900 Hom.: 39128 Cov.: 31

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.895

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.732

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

GnomAD4 genome AF: 0.716 AC: 108809 AN: 152018 Hom.: 39175 Cov.: 31 AF XY: 0.715 AC XY: 53099 AN XY: 74284

African (AFR) AF: 0.672 AC: 27867 AN: 41454

American (AMR) AF: 0.719 AC: 10981 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.895 AC: 3106 AN: 3472

East Asian (EAS) AF: 0.591 AC: 3022 AN: 5112

South Asian (SAS) AF: 0.725 AC: 3497 AN: 4824

European-Finnish (FIN) AF: 0.696 AC: 7367 AN: 10582

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.743 AC: 50537 AN: 67982

Other (OTH) AF: 0.735 AC: 1553 AN: 2112

Alfa AF: 0.653 Hom.: 2123

Bravo AF: 0.717

Asia WGS AF: 0.679 AC: 2364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.80
DANN	Benign	0.38
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs4443391; hg19: chr5-24226892;