5-83877774-C-T

Variant names:

• chr5-83877774-C-T
• rs4552569
• ENST00000824323.1:n.439-12833G>A

Variant summary

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

The ENST00000824323.1(ENSG00000307155):​n.439-12833G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.753 in 152,060 control chromosomes in the GnomAD database, including 43,164 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 0.75 (43164 hom., cov: 32)
• Consequence: ENSG00000307155 ENST00000824323.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 33 publications found

Genes affected

ENSG00000307155 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.782 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
ENSG00000307155	ENST00000824323.1	n.439-12833G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.753 AC: 114425 AN: 151942 Hom.: 43131 Cov.: 32

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.729

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

GnomAD4 genome AF: 0.753 AC: 114504 AN: 152060 Hom.: 43164 Cov.: 32 AF XY: 0.753 AC XY: 56007 AN XY: 74340

African (AFR) AF: 0.784 AC: 32502 AN: 41476

American (AMR) AF: 0.707 AC: 10803 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.768 AC: 2665 AN: 3468

East Asian (EAS) AF: 0.721 AC: 3706 AN: 5138

South Asian (SAS) AF: 0.803 AC: 3876 AN: 4824

European-Finnish (FIN) AF: 0.724 AC: 7656 AN: 10568

Middle Eastern (MID) AF: 0.668 AC: 195 AN: 292

European-Non Finnish (NFE) AF: 0.748 AC: 50869 AN: 67990

Other (OTH) AF: 0.724 AC: 1530 AN: 2112

Alfa AF: 0.748 Hom.: 200199

Bravo AF: 0.747

Asia WGS AF: 0.783 AC: 2724 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.1
DANN	Benign	0.60
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs4552569; hg19: chr5-83173593;