5-180406485-G-A

Variant names:

• chr5-180406485-G-A
• rs12386481
• ENST00000843753.1:n.144+5438C>T

Variant summary

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

The ENST00000843753.1(ENSG00000309762):​n.144+5438C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 151,924 control chromosomes in the GnomAD database, including 21,962 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 0.51 (21962 hom., cov: 32)
• Consequence: ENSG00000309762 ENST00000843753.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.668
• Publications: 7 publications found

Genes affected

ENSG00000309762 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.63 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
ENSG00000309762	ENST00000843753.1	n.144+5438C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78066 AN: 151806 Hom.: 21953 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.514 AC: 78090 AN: 151924 Hom.: 21962 Cov.: 32 AF XY: 0.514 AC XY: 38141 AN XY: 74268

African (AFR) AF: 0.267 AC: 11062 AN: 41376

American (AMR) AF: 0.572 AC: 8720 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1929 AN: 3472

East Asian (EAS) AF: 0.442 AC: 2282 AN: 5164

South Asian (SAS) AF: 0.534 AC: 2570 AN: 4812

European-Finnish (FIN) AF: 0.636 AC: 6723 AN: 10566

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.635 AC: 43167 AN: 67970

Other (OTH) AF: 0.519 AC: 1094 AN: 2108

Alfa AF: 0.598 Hom.: 17149

Bravo AF: 0.496

Asia WGS AF: 0.494 AC: 1713 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	2.3
DANN	Benign	0.30
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs12386481; hg19: chr5-179833485;