2-14837292-C-T

Position:

• chr2-14837292-C-T

Variant summary

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

The ENST00000654007.1(ENSG00000287291):​n.857-123997G>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 0.294 in 151,654 control chromosomes in the GnomAD database, including 7,123 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 (7123 hom., cov: 33)
• Consequence: ENST00000654007.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NBAS	XR_007076390.1	n.7016-58145G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000654007.1	n.857-123997G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44587 AN: 151536 Hom.: 7114 Cov.: 33

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.294 AC: 44615 AN: 151654 Hom.: 7123 Cov.: 33 AF XY: 0.300 AC XY: 22236 AN XY: 74122

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.397

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.434

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.301

Alfa AF: 0.313 Hom.: 980

Bravo AF: 0.280

Asia WGS AF: 0.378 AC: 1315 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1518789; hg19: chr2-14977416;