rs10819795

Positions:

• chr9-100606081-T-A
• chr9-100606081-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 0.0425 in 152,164 control chromosomes in the GnomAD database, including 291 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 0.042 (291 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0425 AC: 6467 AN: 152046 Hom.: 292 Cov.: 33

Gnomad AFR AF: 0.0430

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0312

Gnomad ASJ AF: 0.0219

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.0432

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0228

Gnomad OTH AF: 0.0373

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

GnomAD4 genome AF: 0.0425 AC: 6460 AN: 152164 Hom.: 291 Cov.: 33 AF XY: 0.0467 AC XY: 3470 AN XY: 74374

Gnomad4 AFR AF: 0.0430

Gnomad4 AMR AF: 0.0310

Gnomad4 ASJ AF: 0.0219

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.0432

Gnomad4 NFE AF: 0.0228

Gnomad4 OTH AF: 0.0374

Alfa AF: 0.0120 Hom.: 5

Bravo AF: 0.0390

Asia WGS AF: 0.206 AC: 713 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10819795; hg19: chr9-103368363;