rs1935924

Variant names:

• chr10-52828330-G-A
• rs1935924

Your query was ambiguous. Multiple possible variants found:

• chr10-52828330-G-A
• chr10-52828330-G-C
• chr10-52828330-G-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 0.523 in 128,098 control chromosomes in the GnomAD database, including 17,331 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 0.52 (17331 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.604 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: 0.523 AC: 66933 AN: 128028 Hom.: 17326 Cov.: 24

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.569

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.523 AC: 66942 AN: 128098 Hom.: 17331 Cov.: 24 AF XY: 0.522 AC XY: 32447 AN XY: 62108

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.443

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.587

Gnomad4 SAS AF: 0.580

Gnomad4 FIN AF: 0.644

Gnomad4 NFE AF: 0.609

Gnomad4 OTH AF: 0.542

Alfa AF: 0.548 Hom.: 37245

Bravo AF: 0.423

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.5
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1935924; hg19: chr10-54588090;