rs1838539

Variant names:

• chr10-58839702-G-A
• rs1838539

Your query was ambiguous. Multiple possible variants found:

• chr10-58839702-G-A
• chr10-58839702-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;