rs6872596

Variant names:

• chr5-170084275-C-A
• rs6872596

Your query was ambiguous. Multiple possible variants found:

• chr5-170084275-C-A
• chr5-170084275-C-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 0.298 in 151,968 control chromosomes in the GnomAD database, including 7,755 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 0.30 (7755 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45323 AN: 151850 Hom.: 7749 Cov.: 31

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.298 AC: 45341 AN: 151968 Hom.: 7755 Cov.: 31 AF XY: 0.294 AC XY: 21842 AN XY: 74260

African (AFR) AF: 0.141 AC: 5825 AN: 41452

American (AMR) AF: 0.341 AC: 5209 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1227 AN: 3472

East Asian (EAS) AF: 0.156 AC: 803 AN: 5160

South Asian (SAS) AF: 0.258 AC: 1239 AN: 4808

European-Finnish (FIN) AF: 0.381 AC: 4025 AN: 10564

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25900 AN: 67912

Other (OTH) AF: 0.336 AC: 708 AN: 2106

Alfa AF: 0.343 Hom.: 21380

Bravo AF: 0.292

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.7
DANN	Benign	0.44
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs6872596; hg19: chr5-169511279; COSMIC: COSV56949974;