rs12441867

Variant names:

• chr15-48343856-T-C
• rs12441867

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 0.697 in 152,038 control chromosomes in the GnomAD database, including 39,411 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 0.70 (39411 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.83 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: 0.697 AC: 105945 AN: 151920 Hom.: 39422 Cov.: 31

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.901

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.697 AC: 105950 AN: 152038 Hom.: 39411 Cov.: 31 AF XY: 0.698 AC XY: 51863 AN XY: 74314

African (AFR) AF: 0.432 AC: 17915 AN: 41426

American (AMR) AF: 0.705 AC: 10767 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.812 AC: 2815 AN: 3468

East Asian (EAS) AF: 0.517 AC: 2662 AN: 5150

South Asian (SAS) AF: 0.680 AC: 3280 AN: 4822

European-Finnish (FIN) AF: 0.864 AC: 9148 AN: 10588

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.836 AC: 56827 AN: 67990

Other (OTH) AF: 0.702 AC: 1482 AN: 2110

Alfa AF: 0.779 Hom.: 59200

Bravo AF: 0.675

Asia WGS AF: 0.554 AC: 1929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
DANN	Benign	0.71
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs12441867; hg19: chr15-48636053;