rs7143894

Variant names:

• chr14-57171114-C-T
• rs7143894
• ENST00000825124.1:n.228-6318G>A

Variant summary

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

The ENST00000825124.1(ENSG00000307333):​n.228-6318G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 152,172 control chromosomes in the GnomAD database, including 13,434 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 0.29 (13434 hom., cov: 33)
• Consequence: ENSG00000307333 ENST00000825124.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 6 publications found

Genes affected

ENSG00000307333 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.772 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
ENSG00000307333	ENST00000825124.1	n.228-6318G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43580 AN: 152054 Hom.: 13376 Cov.: 33

Gnomad AFR AF: 0.778

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.0900

Gnomad SAS AF: 0.0435

Gnomad FIN AF: 0.0317

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.0995

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.287 AC: 43693 AN: 152172 Hom.: 13434 Cov.: 33 AF XY: 0.275 AC XY: 20483 AN XY: 74398

African (AFR) AF: 0.779 AC: 32320 AN: 41486

American (AMR) AF: 0.158 AC: 2409 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 586 AN: 3468

East Asian (EAS) AF: 0.0901 AC: 467 AN: 5186

South Asian (SAS) AF: 0.0433 AC: 209 AN: 4828

European-Finnish (FIN) AF: 0.0317 AC: 336 AN: 10602

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.0995 AC: 6765 AN: 68010

Other (OTH) AF: 0.241 AC: 510 AN: 2112

Alfa AF: 0.160 Hom.: 7205

Bravo AF: 0.320

Asia WGS AF: 0.100 AC: 346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.33
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7143894; hg19: chr14-57637832;