rs10867752

Variant names:

• chr9-81400122-C-T
• rs10867752

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.118 in 152,070 control chromosomes in the GnomAD database, including 1,401 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 0.12 (1401 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17916 AN: 151952 Hom.: 1403 Cov.: 32

Gnomad AFR AF: 0.0296

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.0953

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.0434

Gnomad SAS AF: 0.0941

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.118 AC: 17907 AN: 152070 Hom.: 1401 Cov.: 32 AF XY: 0.117 AC XY: 8665 AN XY: 74340

African (AFR) AF: 0.0295 AC: 1225 AN: 41504

American (AMR) AF: 0.0951 AC: 1453 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 563 AN: 3472

East Asian (EAS) AF: 0.0433 AC: 223 AN: 5148

South Asian (SAS) AF: 0.0948 AC: 456 AN: 4808

European-Finnish (FIN) AF: 0.189 AC: 1997 AN: 10566

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11623 AN: 67970

Other (OTH) AF: 0.129 AC: 273 AN: 2114

Alfa AF: 0.152 Hom.: 6804

Bravo AF: 0.108

Asia WGS AF: 0.0630 AC: 220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.57
DANN	Benign	0.27
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs10867752; hg19: chr9-84015037;