rs10511930

chr9-36689990-T-C

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 0.0562 in 152,072 control chromosomes in the GnomAD database, including 685 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 0.056 (685 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.926

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.166 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: 0.0560 AC: 8513 AN: 151954 Hom.: 681 Cov.: 31

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0280

Gnomad ASJ AF: 0.0288

Gnomad EAS AF: 0.0322

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.000188

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.00294

Gnomad OTH AF: 0.0451

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

GnomAD4 genome AF: 0.0562 AC: 8541 AN: 152072 Hom.: 685 Cov.: 31 AF XY: 0.0550 AC XY: 4090 AN XY: 74318

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.0280

Gnomad4 ASJ AF: 0.0288

Gnomad4 EAS AF: 0.0321

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.000188

Gnomad4 NFE AF: 0.00296

Gnomad4 OTH AF: 0.0503

Alfa AF: 0.0355 Hom.: 56

Bravo AF: 0.0611

Asia WGS AF: 0.0710 AC: 248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	7.3
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511930; hg19: chr9-36689987;