5-5822534-C-T

Variant names:

• chr5-5822534-C-T
• rs3852160
• ENST00000776898.1:n.309-6839C>T

Variant summary

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

The ENST00000776898.1(ENSG00000301190):​n.309-6839C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 152,008 control chromosomes in the GnomAD database, including 29,581 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 0.62 (29581 hom., cov: 32)
• Consequence: ENSG00000301190 ENST00000776898.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.888
• Publications: 3 publications found

Genes affected

ENSG00000301190 (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 (AFR) allele frequency at 95% confidence interval = 0.674 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
ENSG00000301190	ENST00000776898.1	n.309-6839C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.623 AC: 94580 AN: 151888 Hom.: 29552 Cov.: 32

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.623 AC: 94653 AN: 152008 Hom.: 29581 Cov.: 32 AF XY: 0.624 AC XY: 46342 AN XY: 74292

African (AFR) AF: 0.680 AC: 28197 AN: 41436

American (AMR) AF: 0.654 AC: 9995 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1893 AN: 3470

East Asian (EAS) AF: 0.578 AC: 2986 AN: 5166

South Asian (SAS) AF: 0.571 AC: 2751 AN: 4818

European-Finnish (FIN) AF: 0.617 AC: 6506 AN: 10550

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.592 AC: 40260 AN: 67976

Other (OTH) AF: 0.625 AC: 1322 AN: 2116

Alfa AF: 0.606 Hom.: 40078

Bravo AF: 0.627

Asia WGS AF: 0.611 AC: 2127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.51
DANN	Benign	0.44
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs3852160; hg19: chr5-5822647;