9-75668508-C-T

Variant names:

• chr9-75668508-C-T
• rs1360003

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 0.74 in 152,038 control chromosomes in the GnomAD database, including 41,848 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 0.74 (41848 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.878 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: 0.740 AC: 112377 AN: 151920 Hom.: 41829 Cov.: 33

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.900

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.754

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

GnomAD4 genome AF: 0.740 AC: 112443 AN: 152038 Hom.: 41848 Cov.: 33 AF XY: 0.743 AC XY: 55181 AN XY: 74288

African (AFR) AF: 0.657 AC: 27232 AN: 41472

American (AMR) AF: 0.799 AC: 12181 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.692 AC: 2399 AN: 3468

East Asian (EAS) AF: 0.900 AC: 4640 AN: 5158

South Asian (SAS) AF: 0.798 AC: 3845 AN: 4820

European-Finnish (FIN) AF: 0.763 AC: 8080 AN: 10590

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.759 AC: 51571 AN: 67964

Other (OTH) AF: 0.754 AC: 1589 AN: 2108

Alfa AF: 0.752 Hom.: 32104

Bravo AF: 0.740

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.4
DANN	Benign	0.35
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs1360003; hg19: chr9-78283424;