9-117702042-T-C

Variant names:

• chr9-117702042-T-C
• rs10116253

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 0.279 in 152,106 control chromosomes in the GnomAD database, including 6,004 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 0.28 (6004 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910
• Publications: 57 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 (EAS) allele frequency at 95% confidence interval = 0.366 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: 0.279 AC: 42405 AN: 151988 Hom.: 5997 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.279 AC: 42461 AN: 152106 Hom.: 6004 Cov.: 32 AF XY: 0.283 AC XY: 21067 AN XY: 74328

African (AFR) AF: 0.287 AC: 11911 AN: 41492

American (AMR) AF: 0.291 AC: 4442 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1087 AN: 3470

East Asian (EAS) AF: 0.380 AC: 1962 AN: 5164

South Asian (SAS) AF: 0.262 AC: 1258 AN: 4808

European-Finnish (FIN) AF: 0.348 AC: 3687 AN: 10582

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17279 AN: 68004

Other (OTH) AF: 0.271 AC: 573 AN: 2112

Alfa AF: 0.228 Hom.: 1097

Bravo AF: 0.275

Asia WGS AF: 0.301 AC: 1046 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	4.7
DANN	Benign	0.52
PhyloP100		0.091

Splicing

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

Other links and lift over

dbSNP: rs10116253; hg19: chr9-120464320;