rs13088214

Variant names:

• chr3-12446328-T-C
• rs13088214

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 0.338 in 152,050 control chromosomes in the GnomAD database, including 9,662 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 0.34 (9662 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.488 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: 0.338 AC: 51324 AN: 151932 Hom.: 9660 Cov.: 32

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.0268

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.338 AC: 51375 AN: 152050 Hom.: 9662 Cov.: 32 AF XY: 0.335 AC XY: 24923 AN XY: 74312

African (AFR) AF: 0.493 AC: 20451 AN: 41452

American (AMR) AF: 0.334 AC: 5104 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1124 AN: 3464

East Asian (EAS) AF: 0.0268 AC: 139 AN: 5182

South Asian (SAS) AF: 0.202 AC: 975 AN: 4816

European-Finnish (FIN) AF: 0.310 AC: 3276 AN: 10554

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18979 AN: 67980

Other (OTH) AF: 0.309 AC: 654 AN: 2114

Alfa AF: 0.294 Hom.: 27616

Bravo AF: 0.351

Asia WGS AF: 0.130 AC: 455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.6
DANN	Benign	0.64
PhyloP100		0.030

Splicing

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

Other links and lift over

dbSNP: rs13088214; hg19: chr3-12487827;