rs12892356

Variant names:

• chr14-98030842-G-T
• rs12892356

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 0.0697 in 152,274 control chromosomes in the GnomAD database, including 502 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 0.070 (502 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.123 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: 0.0696 AC: 10587 AN: 152156 Hom.: 500 Cov.: 33

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0512

Gnomad ASJ AF: 0.0352

Gnomad EAS AF: 0.0877

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0656

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0376

Gnomad OTH AF: 0.0679

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

GnomAD4 genome AF: 0.0697 AC: 10612 AN: 152274 Hom.: 502 Cov.: 33 AF XY: 0.0719 AC XY: 5352 AN XY: 74454

African (AFR) AF: 0.126 AC: 5232 AN: 41544

American (AMR) AF: 0.0512 AC: 783 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0352 AC: 122 AN: 3468

East Asian (EAS) AF: 0.0879 AC: 455 AN: 5174

South Asian (SAS) AF: 0.122 AC: 587 AN: 4826

European-Finnish (FIN) AF: 0.0656 AC: 696 AN: 10612

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0376 AC: 2561 AN: 68026

Other (OTH) AF: 0.0681 AC: 144 AN: 2114

Alfa AF: 0.0515 Hom.: 207

Bravo AF: 0.0673

Asia WGS AF: 0.102 AC: 355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.1
DANN	Benign	0.76
PhyloP100		0.048

Splicing

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

Other links and lift over

dbSNP: rs12892356; hg19: chr14-98497179;