rs889312

chr5-56736057-C-Achr5-56736057-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.682 in 151,942 control chromosomes in the GnomAD database, including 35,558 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 0.68 (35558 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.712 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: 0.682 AC: 103504 AN: 151824 Hom.: 35543 Cov.: 31

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.767

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.682 AC: 103549 AN: 151942 Hom.: 35558 Cov.: 31 AF XY: 0.678 AC XY: 50338 AN XY: 74262

Gnomad4 AFR AF: 0.665

Gnomad4 AMR AF: 0.610

Gnomad4 ASJ AF: 0.682

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.612

Gnomad4 FIN AF: 0.767

Gnomad4 NFE AF: 0.717

Gnomad4 OTH AF: 0.669

Alfa AF: 0.698 Hom.: 76889

Bravo AF: 0.668

Asia WGS AF: 0.548 AC: 1904 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	18
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs889312; hg19: chr5-56031884;