rs6594987

Variant names:

• chr5-116892616-A-C
• rs6594987

Your query was ambiguous. Multiple possible variants found:

• chr5-116892616-A-C
• chr5-116892616-A-G
• chr5-116892616-A-T

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 0.802 in 152,196 control chromosomes in the GnomAD database, including 49,026 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 0.80 (49026 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.82 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: 0.802 AC: 121951 AN: 152078 Hom.: 48975 Cov.: 34

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.797

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.790

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

GnomAD4 genome AF: 0.802 AC: 122063 AN: 152196 Hom.: 49026 Cov.: 34 AF XY: 0.805 AC XY: 59885 AN XY: 74422

Gnomad4 AFR AF: 0.783

Gnomad4 AMR AF: 0.769

Gnomad4 ASJ AF: 0.797

Gnomad4 EAS AF: 0.841

Gnomad4 SAS AF: 0.828

Gnomad4 FIN AF: 0.852

Gnomad4 NFE AF: 0.810

Gnomad4 OTH AF: 0.793

Alfa AF: 0.807 Hom.: 101072

Bravo AF: 0.792

Asia WGS AF: 0.830 AC: 2886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.7
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6594987; hg19: chr5-116228312;