5-108498546-C-T

Variant names:

• chr5-108498546-C-T
• rs4571457
• ENST00000829682.1:n.178-16798G>A

Variant summary

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

The ENST00000829682.1(ENSG00000307906):​n.178-16798G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 151,926 control chromosomes in the GnomAD database, including 25,409 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 0.57 (25409 hom., cov: 32)
• Consequence: ENSG00000307906 ENST00000829682.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 4 publications found

Genes affected

ENSG00000307906 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.624 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
ENSG00000307906	ENST00000829682.1	n.178-16798G>A		intron_variant	Intron 2 of 3
ENSG00000307906	ENST00000829683.1	n.110-16798G>A		intron_variant	Intron 1 of 2
ENSG00000307920	ENST00000829859.1	n.221+12676C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.573 AC: 86985 AN: 151808 Hom.: 25399 Cov.: 32

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.573 AC: 87034 AN: 151926 Hom.: 25409 Cov.: 32 AF XY: 0.568 AC XY: 42179 AN XY: 74278

African (AFR) AF: 0.487 AC: 20164 AN: 41408

American (AMR) AF: 0.564 AC: 8602 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.730 AC: 2530 AN: 3468

East Asian (EAS) AF: 0.423 AC: 2191 AN: 5174

South Asian (SAS) AF: 0.593 AC: 2856 AN: 4820

European-Finnish (FIN) AF: 0.556 AC: 5874 AN: 10560

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.629 AC: 42738 AN: 67936

Other (OTH) AF: 0.589 AC: 1242 AN: 2108

Alfa AF: 0.601 Hom.: 48341

Bravo AF: 0.567

Asia WGS AF: 0.506 AC: 1760 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	0.50
DANN	Benign	0.32
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4571457; hg19: chr5-107834247;