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. The variant received -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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.320 AC: 13256 AN: 41476

American (AMR) AF: 0.370 AC: 5653 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1564 AN: 3468

East Asian (EAS) AF: 0.479 AC: 2473 AN: 5168

South Asian (SAS) AF: 0.473 AC: 2285 AN: 4826

European-Finnish (FIN) AF: 0.318 AC: 3358 AN: 10550

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24205 AN: 67974

Other (OTH) AF: 0.386 AC: 816 AN: 2112

Alfa AF: 0.359 Hom.: 30790

Bravo AF: 0.354

Asia WGS AF: 0.455 AC: 1571 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	7.7
DANN	Benign	0.90
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs12895203; hg19: chr14-66339018;