chr9-102740216-T-C

Variant names:

• chr9-102740216-T-C
• rs10990268

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 0.17 in 152,078 control chromosomes in the GnomAD database, including 2,386 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 0.17 (2386 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.535
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.267 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: 0.170 AC: 25803 AN: 151960 Hom.: 2386 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.170 AC: 25822 AN: 152078 Hom.: 2386 Cov.: 32 AF XY: 0.179 AC XY: 13290 AN XY: 74352

African (AFR) AF: 0.191 AC: 7913 AN: 41478

American (AMR) AF: 0.234 AC: 3579 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 522 AN: 3470

East Asian (EAS) AF: 0.197 AC: 1017 AN: 5164

South Asian (SAS) AF: 0.279 AC: 1347 AN: 4830

European-Finnish (FIN) AF: 0.194 AC: 2051 AN: 10572

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.131 AC: 8905 AN: 67984

Other (OTH) AF: 0.179 AC: 377 AN: 2108

Alfa AF: 0.141 Hom.: 5131

Bravo AF: 0.171

Asia WGS AF: 0.224 AC: 774 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.40
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs10990268; hg19: chr9-105502498;