rs10491207

Variant names:

• chr10-57971738-T-G
• rs10491207

Variant summary

Our verdict is Benign. The variant received -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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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 AC: 0.241885 AN: 0.241885

Gnomad4 AMR AF: 0.0366 AC: 0.0366061 AN: 0.0366061

Gnomad4 ASJ AF: 0.0432 AC: 0.0432028 AN: 0.0432028

Gnomad4 EAS AF: 0.000193 AC: 0.000193349 AN: 0.000193349

Gnomad4 SAS AF: 0.00871 AC: 0.00871369 AN: 0.00871369

Gnomad4 FIN AF: 0.00349 AC: 0.00349122 AN: 0.00349122

Gnomad4 NFE AF: 0.0130 AC: 0.0130418 AN: 0.0130418

Gnomad4 OTH AF: 0.0677 AC: 0.0677083 AN: 0.0677083

Alfa AF: 0.0612 Hom.: 116

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;