rs12883508

Variant names:

• chr14-42362695-T-C
• rs12883508

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.0574

Gnomad4 AMR AF: 0.0400

Gnomad4 ASJ AF: 0.0644

Gnomad4 EAS AF: 0.0141

Gnomad4 SAS AF: 0.0112

Gnomad4 FIN AF: 0.0567

Gnomad4 NFE AF: 0.0623

Gnomad4 OTH AF: 0.0504

Alfa AF: 0.0565 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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12883508; hg19: chr14-42831898;