rs853180

Positions:

• chr5-143249878-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;