rs6596684

Variant names:

• chr5-106609232-G-A
• rs6596684

Your query was ambiguous. Multiple possible variants found:

• chr5-106609232-G-A
• chr5-106609232-G-C
• chr5-106609232-G-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 0.603 in 151,892 control chromosomes in the GnomAD database, including 28,693 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 0.60 (28693 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.86
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.604 AC: 91622 AN: 151776 Hom.: 28699 Cov.: 31

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.733

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.603 AC: 91622 AN: 151892 Hom.: 28693 Cov.: 31 AF XY: 0.599 AC XY: 44475 AN XY: 74252

African (AFR) AF: 0.437 AC: 18057 AN: 41352

American (AMR) AF: 0.655 AC: 10008 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2135 AN: 3468

East Asian (EAS) AF: 0.556 AC: 2870 AN: 5158

South Asian (SAS) AF: 0.387 AC: 1864 AN: 4820

European-Finnish (FIN) AF: 0.706 AC: 7459 AN: 10558

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47155 AN: 67956

Other (OTH) AF: 0.588 AC: 1237 AN: 2104

Alfa AF: 0.657 Hom.: 58535

Bravo AF: 0.596

Asia WGS AF: 0.466 AC: 1624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.12
DANN	Benign	0.56
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs6596684; hg19: chr5-105944933; COSMIC: COSV50462496;