rs9965625

Variant names:

• chr18-55163048-A-G
• rs9965625

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.543 in 152,002 control chromosomes in the GnomAD database, including 22,753 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 0.54 (22753 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.53

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.568 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: 0.543 AC: 82514 AN: 151884 Hom.: 22740 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.543 AC: 82552 AN: 152002 Hom.: 22753 Cov.: 32 AF XY: 0.535 AC XY: 39728 AN XY: 74290

Gnomad4 AFR AF: 0.565

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.374

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.573

Gnomad4 OTH AF: 0.546

Alfa AF: 0.553 Hom.: 3629

Bravo AF: 0.545

Asia WGS AF: 0.397 AC: 1379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0030
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9965625; hg19: chr18-52830279;