rs1147443

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

ENSG00000258847 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000258847	ENST00000775253.1	n.124-13393G>A		intron_variant	Intron 1 of 3
ENSG00000258847	ENST00000775254.1	n.123-13393G>A		intron_variant	Intron 1 of 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

African (AFR) AF: 0.296 AC: 12260 AN: 41474

American (AMR) AF: 0.244 AC: 3729 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 568 AN: 3468

East Asian (EAS) AF: 0.136 AC: 704 AN: 5170

South Asian (SAS) AF: 0.196 AC: 942 AN: 4814

European-Finnish (FIN) AF: 0.299 AC: 3165 AN: 10576

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17441 AN: 67966

Other (OTH) AF: 0.243 AC: 514 AN: 2112

Alfa AF: 0.251 Hom.: 8337

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
PhyloP100		-0.068

Splicing

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

Other links and lift over

dbSNP: rs1147443; hg19: chr14-66468761;