rs751006

chr10-25816546-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.322 in 151,996 control chromosomes in the GnomAD database, including 7,946 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 0.32 (7946 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.97

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.401 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: 0.322 AC: 48885 AN: 151882 Hom.: 7931 Cov.: 31

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.322 AC: 48947 AN: 151996 Hom.: 7946 Cov.: 31 AF XY: 0.319 AC XY: 23685 AN XY: 74274

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.336

Alfa AF: 0.330 Hom.: 2101

Bravo AF: 0.326

Asia WGS AF: 0.380 AC: 1321 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
Cadd	Benign	19
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs751006; hg19: chr10-26105475;