chr2-14837262-T-A

Position:

• chr2-14837262-T-A

Variant summary

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

The ENST00000654007.1(ENSG00000287291):​n.857-123967A>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 0.294 in 151,788 control chromosomes in the GnomAD database, including 7,124 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 (7124 hom., cov: 33)
• Consequence: ENST00000654007.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.413

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• 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.7016-58115A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000654007.1	n.857-123967A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44585 AN: 151670 Hom.: 7115 Cov.: 33

Gnomad AFR AF: 0.174

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: 0.433

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: 44613 AN: 151788 Hom.: 7124 Cov.: 33 AF XY: 0.300 AC XY: 22225 AN XY: 74188

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.397

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.301

Alfa AF: 0.313 Hom.: 979

Bravo AF: 0.280

Asia WGS AF: 0.377 AC: 1310 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1518790; hg19: chr2-14977386;