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. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.783 AC: 32509 AN: 41512

American (AMR) AF: 0.769 AC: 11756 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.797 AC: 2764 AN: 3470

East Asian (EAS) AF: 0.841 AC: 4359 AN: 5182

South Asian (SAS) AF: 0.828 AC: 4000 AN: 4830

European-Finnish (FIN) AF: 0.852 AC: 9036 AN: 10600

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.810 AC: 55082 AN: 68008

Other (OTH) AF: 0.793 AC: 1674 AN: 2110

Alfa AF: 0.806 Hom.: 211102

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
PhyloP100		0.072

Splicing

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

Other links and lift over

dbSNP: rs6594987; hg19: chr5-116228312;