9-10686696-T-C

Variant names:

• chr9-10686696-T-C
• rs4623487

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 0.0431 in 152,274 control chromosomes in the GnomAD database, including 808 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 0.043 (808 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.924
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.244 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: 0.0430 AC: 6543 AN: 152156 Hom.: 803 Cov.: 32

Gnomad AFR AF: 0.00921

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.00461

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.00574

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00537

Gnomad OTH AF: 0.0416

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

GnomAD4 genome AF: 0.0431 AC: 6565 AN: 152274 Hom.: 808 Cov.: 32 AF XY: 0.0497 AC XY: 3697 AN XY: 74454

African (AFR) AF: 0.00928 AC: 386 AN: 41578

American (AMR) AF: 0.236 AC: 3604 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.00461 AC: 16 AN: 3468

East Asian (EAS) AF: 0.256 AC: 1322 AN: 5170

South Asian (SAS) AF: 0.147 AC: 706 AN: 4816

European-Finnish (FIN) AF: 0.00574 AC: 61 AN: 10628

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00537 AC: 365 AN: 68020

Other (OTH) AF: 0.0426 AC: 90 AN: 2112

Alfa AF: 0.0238 Hom.: 45

Bravo AF: 0.0581

Asia WGS AF: 0.190 AC: 660 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.21
DANN	Benign	0.67
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs4623487; hg19: chr9-10686696;