rs12883508

Variant names:

• chr14-42362695-T-C
• rs12883508

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 0.0548 in 150,282 control chromosomes in the GnomAD database, including 254 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 0.055 (254 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.385
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0607 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: 0.0548 AC: 8236 AN: 150162 Hom.: 255 Cov.: 30

Gnomad AFR AF: 0.0575

Gnomad AMI AF: 0.0485

Gnomad AMR AF: 0.0400

Gnomad ASJ AF: 0.0644

Gnomad EAS AF: 0.0141

Gnomad SAS AF: 0.0114

Gnomad FIN AF: 0.0567

Gnomad MID AF: 0.0160

Gnomad NFE AF: 0.0623

Gnomad OTH AF: 0.0510

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

GnomAD4 genome AF: 0.0548 AC: 8237 AN: 150282 Hom.: 254 Cov.: 30 AF XY: 0.0520 AC XY: 3815 AN XY: 73364

African (AFR) AF: 0.0574 AC: 2339 AN: 40760

American (AMR) AF: 0.0400 AC: 604 AN: 15114

Ashkenazi Jewish (ASJ) AF: 0.0644 AC: 222 AN: 3448

East Asian (EAS) AF: 0.0141 AC: 71 AN: 5020

South Asian (SAS) AF: 0.0112 AC: 53 AN: 4726

European-Finnish (FIN) AF: 0.0567 AC: 583 AN: 10288

Middle Eastern (MID) AF: 0.0171 AC: 5 AN: 292

European-Non Finnish (NFE) AF: 0.0623 AC: 4211 AN: 67644

Other (OTH) AF: 0.0504 AC: 105 AN: 2082

Alfa AF: 0.0567 Hom.: 50

Bravo AF: 0.0542

Asia WGS AF: 0.0160 AC: 58 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.3
DANN	Benign	0.47
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs12883508; hg19: chr14-42831898;