rs10079252

Variant names:

• chr5-18584282-A-G
• rs10079252

Your query was ambiguous. Multiple possible variants found:

• chr5-18584282-A-G
• chr5-18584282-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 0.47 in 151,656 control chromosomes in the GnomAD database, including 17,189 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 0.47 (17189 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.521 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: 0.470 AC: 71294 AN: 151542 Hom.: 17188 Cov.: 31

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.470 AC: 71326 AN: 151656 Hom.: 17189 Cov.: 31 AF XY: 0.464 AC XY: 34364 AN XY: 74056

African (AFR) AF: 0.408 AC: 16867 AN: 41318

American (AMR) AF: 0.374 AC: 5687 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1801 AN: 3464

East Asian (EAS) AF: 0.512 AC: 2645 AN: 5170

South Asian (SAS) AF: 0.383 AC: 1843 AN: 4808

European-Finnish (FIN) AF: 0.506 AC: 5290 AN: 10456

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.526 AC: 35697 AN: 67914

Other (OTH) AF: 0.486 AC: 1023 AN: 2104

Alfa AF: 0.470 Hom.: 2650

Bravo AF: 0.460

Asia WGS AF: 0.440 AC: 1532 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.49
PhyloP100		-0.084

Splicing

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

Other links and lift over

dbSNP: rs10079252; hg19: chr5-18584391; COSMIC: COSV55955213;