rs12965975

Variant names:

• chr18-75597328-C-T
• rs12965975

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 0.541 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.325 AC: 13484 AN: 41428

American (AMR) AF: 0.572 AC: 8735 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1991 AN: 3468

East Asian (EAS) AF: 0.470 AC: 2423 AN: 5154

South Asian (SAS) AF: 0.505 AC: 2431 AN: 4814

European-Finnish (FIN) AF: 0.720 AC: 7602 AN: 10556

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.642 AC: 43635 AN: 67964

Other (OTH) AF: 0.531 AC: 1119 AN: 2108

Alfa AF: 0.598 Hom.: 81896

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
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs12965975; hg19: chr18-73309283;