chr9-90124949-C-T

Variant names:

• chr9-90124949-C-T
• rs2081670

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 0.175 in 152,172 control chromosomes in the GnomAD database, including 2,440 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 0.18 (2440 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.520
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.203 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: 0.175 AC: 26603 AN: 152054 Hom.: 2432 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.175 AC: 26641 AN: 152172 Hom.: 2440 Cov.: 32 AF XY: 0.173 AC XY: 12866 AN XY: 74414

African (AFR) AF: 0.206 AC: 8556 AN: 41492

American (AMR) AF: 0.160 AC: 2446 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 925 AN: 3472

East Asian (EAS) AF: 0.143 AC: 742 AN: 5178

South Asian (SAS) AF: 0.169 AC: 815 AN: 4824

European-Finnish (FIN) AF: 0.154 AC: 1629 AN: 10598

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10961 AN: 68004

Other (OTH) AF: 0.180 AC: 379 AN: 2110

Alfa AF: 0.167 Hom.: 9710

Bravo AF: 0.177

Asia WGS AF: 0.174 AC: 606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.48
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs2081670; hg19: chr9-92887231;