5-151930637-A-G

Variant names:

• chr5-151930637-A-G
• rs2059121

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 0.72 in 152,074 control chromosomes in the GnomAD database, including 40,435 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 0.72 (40435 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.892 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: 0.720 AC: 109400 AN: 151956 Hom.: 40379 Cov.: 32

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.720 AC: 109513 AN: 152074 Hom.: 40435 Cov.: 32 AF XY: 0.714 AC XY: 53082 AN XY: 74330

Gnomad4 AFR AF: 0.899

Gnomad4 AMR AF: 0.689

Gnomad4 ASJ AF: 0.672

Gnomad4 EAS AF: 0.672

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.566

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.698

Alfa AF: 0.670 Hom.: 18272

Bravo AF: 0.740

Asia WGS AF: 0.662 AC: 2303 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.33
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2059121; hg19: chr5-151310198; COSMIC: COSV60212069;