rs8177412

Positions:

• chr5-151020526-T-C

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 0.137 in 728,610 control chromosomes in the GnomAD database, including 7,191 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 0.15 (1861 hom., cov: 33)
  • Exomes 𝑓: 0.13 (5330 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 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: 0.151 AC: 23040 AN: 152154 Hom.: 1858 Cov.: 33

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.0968

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.141

GnomAD4 exome AF: 0.133 AC: 76889 AN: 576338 Hom.: 5330 Cov.: 8 AF XY: 0.135 AC XY: 39814 AN XY: 294246

Gnomad4 AFR exome AF: 0.207

Gnomad4 AMR exome AF: 0.0819

Gnomad4 ASJ exome AF: 0.136

Gnomad4 EAS exome AF: 0.142

Gnomad4 SAS exome AF: 0.168

Gnomad4 FIN exome AF: 0.115

Gnomad4 NFE exome AF: 0.129

Gnomad4 OTH exome AF: 0.137

GnomAD4 genome AF: 0.151 AC: 23065 AN: 152272 Hom.: 1861 Cov.: 33 AF XY: 0.149 AC XY: 11068 AN XY: 74474

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.0967

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.139

Alfa AF: 0.134 Hom.: 2442

Bravo AF: 0.150

Asia WGS AF: 0.154 AC: 536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	13
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8177412; hg19: chr5-150400087;