rs10491207

chr10-57971738-T-G

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 0.0781 in 152,156 control chromosomes in the GnomAD database, including 1,259 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 0.078 (1259 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.238 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: 0.0779 AC: 11841 AN: 152038 Hom.: 1253 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0367

Gnomad ASJ AF: 0.0432

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00912

Gnomad FIN AF: 0.00349

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0130

Gnomad OTH AF: 0.0684

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

GnomAD4 genome AF: 0.0781 AC: 11881 AN: 152156 Hom.: 1259 Cov.: 32 AF XY: 0.0756 AC XY: 5624 AN XY: 74400

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.0366

Gnomad4 ASJ AF: 0.0432

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00871

Gnomad4 FIN AF: 0.00349

Gnomad4 NFE AF: 0.0130

Gnomad4 OTH AF: 0.0677

Alfa AF: 0.0547 Hom.: 94

Bravo AF: 0.0885

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	7.6
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491207; hg19: chr10-59731498;