rs12895203

Variant names:

• chr14-65872300-A-G
• rs12895203

Your query was ambiguous. Multiple possible variants found:

• chr14-65872300-A-G
• chr14-65872300-A-T

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 0.355 in 152,054 control chromosomes in the GnomAD database, including 9,741 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 0.35 (9741 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.463 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: 0.355 AC: 53929 AN: 151938 Hom.: 9733 Cov.: 33

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.355 AC: 53953 AN: 152054 Hom.: 9741 Cov.: 33 AF XY: 0.358 AC XY: 26619 AN XY: 74326

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.386

Alfa AF: 0.364 Hom.: 11506

Bravo AF: 0.354

Asia WGS AF: 0.455 AC: 1571 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	7.7
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12895203; hg19: chr14-66339018;