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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.470 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

Gnomad4 AFR AF: 0.408

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.512

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.506

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.486

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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