chr5-148821037-A-G

Variant names:

• chr5-148821037-A-G
• rs2082395

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.596 in 152,018 control chromosomes in the GnomAD database, including 27,402 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 (27402 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90503 AN: 151900 Hom.: 27383 Cov.: 32

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.621

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.596 AC: 90568 AN: 152018 Hom.: 27402 Cov.: 32 AF XY: 0.603 AC XY: 44834 AN XY: 74316

African (AFR) AF: 0.562 AC: 23287 AN: 41452

American (AMR) AF: 0.708 AC: 10809 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.598 AC: 2075 AN: 3472

East Asian (EAS) AF: 0.744 AC: 3849 AN: 5174

South Asian (SAS) AF: 0.738 AC: 3561 AN: 4824

European-Finnish (FIN) AF: 0.632 AC: 6673 AN: 10564

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.563 AC: 38283 AN: 67948

Other (OTH) AF: 0.626 AC: 1323 AN: 2112

Alfa AF: 0.581 Hom.: 98314

Bravo AF: 0.597

Asia WGS AF: 0.747 AC: 2594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.1
DANN	Benign	0.80
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs2082395; hg19: chr5-148200600;