rs1838539

chr10-58839702-G-Achr10-58839702-G-C

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 0.847 in 151,294 control chromosomes in the GnomAD database, including 55,358 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 0.85 (55358 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.66

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.924 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: 0.847 AC: 128073 AN: 151178 Hom.: 55328 Cov.: 29

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.971

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.971

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.930

Gnomad OTH AF: 0.858

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

GnomAD4 genome AF: 0.847 AC: 128155 AN: 151294 Hom.: 55358 Cov.: 29 AF XY: 0.847 AC XY: 62500 AN XY: 73802

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.910

Gnomad4 ASJ AF: 0.971

Gnomad4 EAS AF: 0.868

Gnomad4 SAS AF: 0.869

Gnomad4 FIN AF: 0.877

Gnomad4 NFE AF: 0.930

Gnomad4 OTH AF: 0.858

Alfa AF: 0.909 Hom.: 35689

Bravo AF: 0.842

Asia WGS AF: 0.833 AC: 2898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.086
Dann	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1838539; hg19: chr10-60599462;