rs1147443

Variant names:

• chr14-66002043-C-T
• rs1147443
• ENST00000554907.1:n.69+2412G>A

Variant summary

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

The ENST00000554907.1(ENSG00000258847):​n.69+2412G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 152,078 control chromosomes in the GnomAD database, including 5,342 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 0.26 (5342 hom., cov: 32)
• Consequence: ENSG00000258847 ENST00000554907.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680

Genes affected

ENSG00000258847 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.291 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
ENSG00000258847	ENST00000554907.1	n.69+2412G>A		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39577 AN: 151960 Hom.: 5340 Cov.: 32

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.260 AC: 39615 AN: 152078 Hom.: 5342 Cov.: 32 AF XY: 0.259 AC XY: 19269 AN XY: 74320

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.243

Alfa AF: 0.249 Hom.: 6536

Bravo AF: 0.257

Asia WGS AF: 0.192 AC: 668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	6.9
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1147443; hg19: chr14-66468761;