rs3846726

Positions:

• chr5-132023306-T-C
• chr5-132023306-T-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 0.501 in 151,778 control chromosomes in the GnomAD database, including 19,251 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 0.50 (19251 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.537

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.524 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: 0.501 AC: 76047 AN: 151660 Hom.: 19244 Cov.: 30

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.501 AC: 76091 AN: 151778 Hom.: 19251 Cov.: 30 AF XY: 0.495 AC XY: 36691 AN XY: 74186

Gnomad4 AFR AF: 0.517

Gnomad4 AMR AF: 0.477

Gnomad4 ASJ AF: 0.474

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.478

Gnomad4 NFE AF: 0.512

Gnomad4 OTH AF: 0.505

Alfa AF: 0.492 Hom.: 8390

Bravo AF: 0.508

Asia WGS AF: 0.438 AC: 1525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.67
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3846726; hg19: chr5-131358999;