rs11594687

chr10-95578774-C-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 0.0787 in 152,256 control chromosomes in the GnomAD database, including 555 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 0.079 (555 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0993 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: 0.0788 AC: 11983 AN: 152138 Hom.: 553 Cov.: 31

Gnomad AFR AF: 0.0384

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0792

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.0389

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0899

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

GnomAD4 genome AF: 0.0787 AC: 11982 AN: 152256 Hom.: 555 Cov.: 31 AF XY: 0.0792 AC XY: 5895 AN XY: 74452

Gnomad4 AFR AF: 0.0383

Gnomad4 AMR AF: 0.0790

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.00309

Gnomad4 SAS AF: 0.0394

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.0894

Alfa AF: 0.0958 Hom.: 161

Bravo AF: 0.0742

Asia WGS AF: 0.0210 AC: 74 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.7
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11594687; hg19: chr10-97338531;