rs10079205

chr5-4197861-C-Gchr5-4197861-C-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 0.855 in 152,154 control chromosomes in the GnomAD database, including 57,480 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 0.86 (57480 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.856 AC: 130124 AN: 152038 Hom.: 57482 Cov.: 33

Gnomad AFR AF: 0.610

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.922

Gnomad ASJ AF: 0.923

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.898

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.953

Gnomad OTH AF: 0.864

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

GnomAD4 genome AF: 0.855 AC: 130148 AN: 152154 Hom.: 57480 Cov.: 33 AF XY: 0.858 AC XY: 63829 AN XY: 74388

Gnomad4 AFR AF: 0.609

Gnomad4 AMR AF: 0.923

Gnomad4 ASJ AF: 0.923

Gnomad4 EAS AF: 0.968

Gnomad4 SAS AF: 0.899

Gnomad4 FIN AF: 0.985

Gnomad4 NFE AF: 0.953

Gnomad4 OTH AF: 0.856

Alfa AF: 0.886 Hom.: 3604

Bravo AF: 0.841

Asia WGS AF: 0.879 AC: 3057 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.42
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10079205; hg19: chr5-4197974;