2-74350270-T-G

Position:

• chr2-74350270-T-G

Variant summary

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

The ENST00000455668.1(NECAP1P2):​n.202T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 161,958 control chromosomes in the GnomAD database, including 2,219 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 0.14 (2005 hom., cov: 33)
  • Exomes 𝑓: 0.16 (214 hom.)
• Consequence: NECAP1P2 ENST00000455668.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287

Genes affected

NECAP1P2 (HGNC:43913): (NECAP endocytosis associated 1 pseudogene 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.457 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
NECAP1P2	ENST00000455668.1	n.202T>G		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21975 AN: 152124 Hom.: 2006 Cov.: 33

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.149

GnomAD4 exome AF: 0.156 AC: 1518 AN: 9716 Hom.: 214 Cov.: 0 AF XY: 0.152 AC XY: 845 AN XY: 5556

Gnomad4 AFR exome AF: 0.118

Gnomad4 AMR exome AF: 0.0565

Gnomad4 ASJ exome AF: 0.125

Gnomad4 EAS exome AF: 0.520

Gnomad4 SAS exome AF: 0.175

Gnomad4 FIN exome AF: 0.112

Gnomad4 NFE exome AF: 0.111

Gnomad4 OTH exome AF: 0.114

GnomAD4 genome AF: 0.144 AC: 21980 AN: 152242 Hom.: 2005 Cov.: 33 AF XY: 0.147 AC XY: 10970 AN XY: 74438

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.473

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.148

Alfa AF: 0.120 Hom.: 203

Bravo AF: 0.148

Asia WGS AF: 0.337 AC: 1168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	1.6
DANN	Benign	0.73

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7581836; hg19: chr2-74577397;