rs10512160

Positions:

• chr9-85242868-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0312 in 152,276 control chromosomes in the GnomAD database, including 68 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 0.031 (68 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.428

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0312 (4748/152276) while in subpopulation SAS AF= 0.0458 (221/4822). AF 95% confidence interval is 0.0409. There are 68 homozygotes in gnomad4. There are 2388 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 68 gene

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: 0.0312 AC: 4742 AN: 152158 Hom.: 68 Cov.: 33

Gnomad AFR AF: 0.0372

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0188

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.0156

Gnomad SAS AF: 0.0460

Gnomad FIN AF: 0.0428

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0294

Gnomad OTH AF: 0.0316

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

GnomAD4 genome AF: 0.0312 AC: 4748 AN: 152276 Hom.: 68 Cov.: 33 AF XY: 0.0321 AC XY: 2388 AN XY: 74466

Gnomad4 AFR AF: 0.0373

Gnomad4 AMR AF: 0.0188

Gnomad4 ASJ AF: 0.0190

Gnomad4 EAS AF: 0.0154

Gnomad4 SAS AF: 0.0458

Gnomad4 FIN AF: 0.0428

Gnomad4 NFE AF: 0.0294

Gnomad4 OTH AF: 0.0313

Alfa AF: 0.0301 Hom.: 9

Bravo AF: 0.0294

Asia WGS AF: 0.0280 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.0
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512160; hg19: chr9-87857783;