9-107940692-C-T

Variant names:

• chr9-107940692-C-T
• rs1888617

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 0.248 in 152,086 control chromosomes in the GnomAD database, including 4,954 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 0.25 (4954 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.283 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: 0.248 AC: 37758 AN: 151968 Hom.: 4960 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.248 AC: 37745 AN: 152086 Hom.: 4954 Cov.: 32 AF XY: 0.245 AC XY: 18230 AN XY: 74350

African (AFR) AF: 0.198 AC: 8208 AN: 41478

American (AMR) AF: 0.250 AC: 3820 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1134 AN: 3468

East Asian (EAS) AF: 0.217 AC: 1119 AN: 5166

South Asian (SAS) AF: 0.107 AC: 516 AN: 4816

European-Finnish (FIN) AF: 0.232 AC: 2451 AN: 10576

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19468 AN: 67982

Other (OTH) AF: 0.296 AC: 626 AN: 2114

Alfa AF: 0.264 Hom.: 4338

Bravo AF: 0.250

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.043
DANN	Benign	0.38
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1888617; hg19: chr9-110702973;