rs12878371

Variant names:

• chr14-103221243-C-T
• rs12878371
• ENST00000742321.1:n.217-5196C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000742321.1(ENSG00000278071):​n.217-5196C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 151,732 control chromosomes in the GnomAD database, including 24,134 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 0.56 (24134 hom., cov: 33)
• Consequence: ENSG00000278071 ENST00000742321.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 4 publications found

Genes affected

ENSG00000278071 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.605 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
ENSG00000278071	ENST00000742321.1	n.217-5196C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85063 AN: 151620 Hom.: 24124 Cov.: 33

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.561 AC: 85112 AN: 151732 Hom.: 24134 Cov.: 33 AF XY: 0.566 AC XY: 41972 AN XY: 74172

African (AFR) AF: 0.612 AC: 25251 AN: 41290

American (AMR) AF: 0.552 AC: 8433 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1852 AN: 3468

East Asian (EAS) AF: 0.601 AC: 3090 AN: 5138

South Asian (SAS) AF: 0.619 AC: 2976 AN: 4806

European-Finnish (FIN) AF: 0.626 AC: 6608 AN: 10556

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35143 AN: 67894

Other (OTH) AF: 0.553 AC: 1164 AN: 2104

Alfa AF: 0.536 Hom.: 8391

Bravo AF: 0.558

Asia WGS AF: 0.524 AC: 1596 AN: 3040

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.6
DANN	Benign	0.79
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs12878371; hg19: chr14-103687580;