rs1746825

Variant names:

• chr9-107386275-T-C
• rs1746825

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 0.659 in 151,992 control chromosomes in the GnomAD database, including 33,727 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 0.66 (33727 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.72 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: 0.659 AC: 100132 AN: 151872 Hom.: 33704 Cov.: 32

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.659 AC: 100191 AN: 151992 Hom.: 33727 Cov.: 32 AF XY: 0.660 AC XY: 48998 AN XY: 74280

African (AFR) AF: 0.528 AC: 21889 AN: 41442

American (AMR) AF: 0.688 AC: 10488 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2358 AN: 3466

East Asian (EAS) AF: 0.666 AC: 3443 AN: 5168

South Asian (SAS) AF: 0.487 AC: 2344 AN: 4818

European-Finnish (FIN) AF: 0.775 AC: 8184 AN: 10566

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.725 AC: 49276 AN: 67976

Other (OTH) AF: 0.659 AC: 1394 AN: 2114

Alfa AF: 0.693 Hom.: 4584

Bravo AF: 0.653

Asia WGS AF: 0.571 AC: 1987 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	7.3
DANN	Benign	0.92
PhyloP100		-0.037

Splicing

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

Other links and lift over

dbSNP: rs1746825; hg19: chr9-110148556;