chr5-29848239-G-A

Variant names:

• chr5-29848239-G-A
• rs1961286

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 0.923 in 152,218 control chromosomes in the GnomAD database, including 65,157 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 0.92 (65157 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250

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 (NFE) allele frequency at 95% confidence interval = 0.958 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: 0.923 AC: 140448 AN: 152100 Hom.: 65119 Cov.: 32

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.960

Gnomad ASJ AF: 0.893

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.941

Gnomad FIN AF: 0.967

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.964

Gnomad OTH AF: 0.930

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

GnomAD4 genome AF: 0.923 AC: 140538 AN: 152218 Hom.: 65157 Cov.: 32 AF XY: 0.923 AC XY: 68639 AN XY: 74402

Gnomad4 AFR AF: 0.846

Gnomad4 AMR AF: 0.960

Gnomad4 ASJ AF: 0.893

Gnomad4 EAS AF: 0.803

Gnomad4 SAS AF: 0.941

Gnomad4 FIN AF: 0.967

Gnomad4 NFE AF: 0.964

Gnomad4 OTH AF: 0.927

Alfa AF: 0.942 Hom.: 8396

Bravo AF: 0.920

Asia WGS AF: 0.884 AC: 3069 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1961286; hg19: chr5-29848346;