rs1147443

chr14-66002043-C-T

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, non coding transcript 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: ENST00000554907.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000554907.1	n.69+2412G>A		intron_variant, non_coding_transcript_variant		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;