chr5-148825809-A-G

Position:

• chr5-148825809-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 0.6 in 152,046 control chromosomes in the GnomAD database, including 27,782 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 0.60 (27775 hom., cov: 32)
  • Exomes 𝑓: 0.59 (7 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.863

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.600 AC: 91077 AN: 151896 Hom.: 27756 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.627

GnomAD4 exome AF: 0.594 AC: 19 AN: 32 Hom.: 7 Cov.: 0 AF XY: 0.654 AC XY: 17 AN XY: 26

Gnomad4 AFR exome AF: 0.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.600 AC: 91141 AN: 152014 Hom.: 27775 Cov.: 32 AF XY: 0.607 AC XY: 45098 AN XY: 74302

Gnomad4 AFR AF: 0.564

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.747

Gnomad4 SAS AF: 0.744

Gnomad4 FIN AF: 0.632

Gnomad4 NFE AF: 0.567

Gnomad4 OTH AF: 0.633

Alfa AF: 0.568 Hom.: 10312

Bravo AF: 0.601

Asia WGS AF: 0.754 AC: 2618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.8
DANN	Benign	0.67

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2053044; hg19: chr5-148205372;