rs889312

Variant names:

• chr5-56736057-C-A
• rs889312

Your query was ambiguous. Multiple possible variants found:

• chr5-56736057-C-A
• chr5-56736057-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;