rs853180

Variant names:

• chr5-143249878-A-G
• rs853180

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0520

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.419

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.297

Alfa AF: 0.343 Hom.: 4629

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs853180; hg19: chr5-142629443;