5-148836839-G-A

Position:

• chr5-148836839-G-A

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 0.666 in 152,058 control chromosomes in the GnomAD database, including 34,069 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 0.67 (34069 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.614

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 (AFR) allele frequency at 95% confidence interval = 0.717 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: 0.666 AC: 101154 AN: 151938 Hom.: 34028 Cov.: 32

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.666 AC: 101241 AN: 152058 Hom.: 34069 Cov.: 32 AF XY: 0.662 AC XY: 49240 AN XY: 74332

Gnomad4 AFR AF: 0.724

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.628

Gnomad4 FIN AF: 0.641

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.678

Alfa AF: 0.659 Hom.: 45655

Bravo AF: 0.664

Asia WGS AF: 0.512 AC: 1780 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	0.16
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6888329; hg19: chr5-148216402;