5-151020289-A-T

Variant names:

• chr5-151020289-A-T
• rs8177409

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 281,296 control chromosomes in the GnomAD database, including 2,797 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 (1787 hom., cov: 33)
  • Exomes 𝑓: 0.12 (1010 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22584 AN: 152170 Hom.: 1785 Cov.: 33

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.0951

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.139

GnomAD4 exome AF: 0.123 AC: 15817 AN: 129008 Hom.: 1010 AF XY: 0.124 AC XY: 8098 AN XY: 65446

Gnomad4 AFR exome AF: 0.207

Gnomad4 AMR exome AF: 0.0807

Gnomad4 ASJ exome AF: 0.134

Gnomad4 EAS exome AF: 0.119

Gnomad4 SAS exome AF: 0.123

Gnomad4 FIN exome AF: 0.0997

Gnomad4 NFE exome AF: 0.122

Gnomad4 OTH exome AF: 0.128

GnomAD4 genome AF: 0.148 AC: 22608 AN: 152288 Hom.: 1787 Cov.: 33 AF XY: 0.145 AC XY: 10806 AN XY: 74464

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.0949

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.137

Alfa AF: 0.0666 Hom.: 80

Bravo AF: 0.148

Asia WGS AF: 0.139 AC: 486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.7
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8177409; hg19: chr5-150399850;