rs10816519

Positions:

• chr9-107483703-T-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The variant allele was found at a frequency of 0.0107 in 152,348 control chromosomes in the GnomAD database, including 14 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 0.011 (14 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BS2: High Homozygotes in GnomAd4 at 14 gene

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: 0.0107 AC: 1624 AN: 152230 Hom.: 14 Cov.: 33

Gnomad AFR AF: 0.00396

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.00687

Gnomad ASJ AF: 0.0179

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0124

Gnomad FIN AF: 0.0134

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0153

Gnomad OTH AF: 0.0162

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

GnomAD4 genome AF: 0.0107 AC: 1628 AN: 152348 Hom.: 14 Cov.: 33 AF XY: 0.0106 AC XY: 787 AN XY: 74510

Gnomad4 AFR AF: 0.00399

Gnomad4 AMR AF: 0.00686

Gnomad4 ASJ AF: 0.0179

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0124

Gnomad4 FIN AF: 0.0134

Gnomad4 NFE AF: 0.0153

Gnomad4 OTH AF: 0.0170

Alfa AF: 0.0143 Hom.: 23

Bravo AF: 0.0101

Asia WGS AF: 0.00520 AC: 18 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	16
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10816519; hg19: chr9-110245984;