rs12100904

Positions:

• 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 ENST00000700834.1(ENSG00000258342):​n.351+17190A>G variant causes a intron, non coding transcript 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: ENST00000700834.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000700834.1	n.351+17190A>G		intron_variant, non_coding_transcript_variant

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;