rs853180

Variant names:

• chr5-143249878-A-G
• rs853180
• ENST00000724474.1:n.*123A>G

Variant summary

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

The ENST00000724474.1(ENSG00000294576):​n.*123A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 152,002 control chromosomes in the GnomAD database, including 7,939 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 0.31 (7939 hom., cov: 31)
• Consequence: ENSG00000294576 ENST00000724474.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0520
• Publications: 7 publications found

Genes affected

ENSG00000294576 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.37 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
ENSG00000294576	ENST00000724474.1	n.*123A>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47254 AN: 151884 Hom.: 7927 Cov.: 31

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.311 AC: 47306 AN: 152002 Hom.: 7939 Cov.: 31 AF XY: 0.309 AC XY: 22924 AN XY: 74282

African (AFR) AF: 0.214 AC: 8867 AN: 41446

American (AMR) AF: 0.268 AC: 4098 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 829 AN: 3466

East Asian (EAS) AF: 0.257 AC: 1330 AN: 5178

South Asian (SAS) AF: 0.238 AC: 1148 AN: 4814

European-Finnish (FIN) AF: 0.419 AC: 4422 AN: 10564

Middle Eastern (MID) AF: 0.267 AC: 78 AN: 292

European-Non Finnish (NFE) AF: 0.374 AC: 25432 AN: 67952

Other (OTH) AF: 0.297 AC: 625 AN: 2104

Alfa AF: 0.343 Hom.: 5161

Bravo AF: 0.298

Asia WGS AF: 0.283 AC: 987 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.56
PhyloP100		-0.052

Splicing

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

Other links and lift over

dbSNP: rs853180; hg19: chr5-142629443;