2-16278385-C-T

Position:

• chr2-16278385-C-T

Variant summary

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

The ENST00000420404.2(ENSG00000228876):​n.965+49119C>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 0.54 in 152,002 control chromosomes in the GnomAD database, including 23,162 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 0.54 (23151 hom., cov: 31)
  • Exomes 𝑓: 0.53 (11 hom.)
• Consequence: ENST00000420404.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66

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 = 0.806 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
	ENST00000420404.2	n.965+49119C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.540 AC: 81950 AN: 151804 Hom.: 23126 Cov.: 31

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.740

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.498

GnomAD4 exome AF: 0.525 AC: 42 AN: 80 Hom.: 11 AF XY: 0.519 AC XY: 27 AN XY: 52

Gnomad4 AFR exome AF: 0.750

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.469

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.540 AC: 82023 AN: 151922 Hom.: 23151 Cov.: 31 AF XY: 0.547 AC XY: 40591 AN XY: 74254

Gnomad4 AFR AF: 0.654

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.491

Gnomad4 EAS AF: 0.826

Gnomad4 SAS AF: 0.741

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.448

Gnomad4 OTH AF: 0.503

Alfa AF: 0.459 Hom.: 26431

Bravo AF: 0.543

Asia WGS AF: 0.780 AC: 2711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.36
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs340767; hg19: chr2-16459653;