rs925587

Positions:

• chr10-47438699-G-A

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 0.3 in 152,042 control chromosomes in the GnomAD database, including 8,962 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 0.30 (8962 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45656 AN: 151926 Hom.: 8961 Cov.: 32

Gnomad AFR AF: 0.0828

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.0435

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.300 AC: 45650 AN: 152042 Hom.: 8962 Cov.: 32 AF XY: 0.297 AC XY: 22090 AN XY: 74308

Gnomad4 AFR AF: 0.0827

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.0434

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.305

Alfa AF: 0.383 Hom.: 2583

Bravo AF: 0.280

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.2
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs925587; hg19: chr10-48300663;