rs12965975

Variant names:

• chr18-75597328-C-T
• rs12965975

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 0.541 in 151,968 control chromosomes in the GnomAD database, including 23,925 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 (23925 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.696

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.637 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: 0.542 AC: 82255 AN: 151850 Hom.: 23916 Cov.: 31

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.541 AC: 82276 AN: 151968 Hom.: 23925 Cov.: 31 AF XY: 0.543 AC XY: 40366 AN XY: 74286

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.572

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.470

Gnomad4 SAS AF: 0.505

Gnomad4 FIN AF: 0.720

Gnomad4 NFE AF: 0.642

Gnomad4 OTH AF: 0.531

Alfa AF: 0.615 Hom.: 55139

Bravo AF: 0.520

Asia WGS AF: 0.470 AC: 1634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.8
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12965975; hg19: chr18-73309283;