9-90647919-T-C

Variant names:

• chr9-90647919-T-C
• rs689687

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 0.14 in 152,130 control chromosomes in the GnomAD database, including 1,925 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 0.14 (1925 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.351 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: 0.140 AC: 21288 AN: 152012 Hom.: 1928 Cov.: 32

Gnomad AFR AF: 0.0339

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.140 AC: 21284 AN: 152130 Hom.: 1925 Cov.: 32 AF XY: 0.141 AC XY: 10461 AN XY: 74356

African (AFR) AF: 0.0338 AC: 1402 AN: 41536

American (AMR) AF: 0.174 AC: 2658 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 549 AN: 3464

East Asian (EAS) AF: 0.365 AC: 1878 AN: 5152

South Asian (SAS) AF: 0.103 AC: 499 AN: 4822

European-Finnish (FIN) AF: 0.200 AC: 2109 AN: 10560

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11699 AN: 67992

Other (OTH) AF: 0.123 AC: 260 AN: 2112

Alfa AF: 0.148 Hom.: 2871

Bravo AF: 0.136

Asia WGS AF: 0.217 AC: 756 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	2.2
DANN	Benign	0.74
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs689687; hg19: chr9-93410201;