rs1254601

Positions:

• chr14-52312827-G-A

Variant summary

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

The ENST00000691625.2(ENSG00000289424):​n.405+9C>T 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 0.446 in 152,016 control chromosomes in the GnomAD database, including 17,739 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 0.45 (17739 hom., cov: 31)
• Consequence: ENST00000691625.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.159

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000691625.2	n.405+9C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67888 AN: 151898 Hom.: 17748 Cov.: 31

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.446 AC: 67869 AN: 152016 Hom.: 17739 Cov.: 31 AF XY: 0.439 AC XY: 32617 AN XY: 74292

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.564

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.470

Alfa AF: 0.548 Hom.: 18628

Bravo AF: 0.423

Asia WGS AF: 0.311 AC: 1081 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.0
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1254601; hg19: chr14-52779545;