rs12100904

Variant names:

• chr14-36015774-A-G
• rs12100904
• ENST00000550089.2:n.463+17190A>G

Your query was ambiguous. Multiple possible variants found:

• chr14-36015774-A-G
• chr14-36015774-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000550089.2(ENSG00000258342):​n.463+17190A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,960 control chromosomes in the GnomAD database, including 14,897 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 0.43 (14897 hom., cov: 32)
• Consequence: ENSG00000258342 ENST00000550089.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50

Genes affected

ENSG00000258342 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.592 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
ENSG00000258342	ENST00000550089.2	n.463+17190A>G		intron_variant	Intron 3 of 4	3
ENSG00000258342	ENST00000660969.2	n.515+17190A>G		intron_variant	Intron 3 of 3
ENSG00000258342	ENST00000662718.1	n.256+17190A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.435 AC: 65984 AN: 151842 Hom.: 14877 Cov.: 32

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.435 AC: 66047 AN: 151960 Hom.: 14897 Cov.: 32 AF XY: 0.439 AC XY: 32610 AN XY: 74246

Gnomad4 AFR AF: 0.497

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.610

Gnomad4 SAS AF: 0.498

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.440

Alfa AF: 0.410 Hom.: 2198

Bravo AF: 0.445

Asia WGS AF: 0.533 AC: 1856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.1
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12100904; hg19: chr14-36484980;