rs7581836

Variant names:

• chr2-74350270-T-G
• rs7581836
• ENST00000451608.2:n.*240-7733A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000451608.2(ENSG00000264324):​n.*240-7733A>C variant causes a intron 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: ENSG00000264324 ENST00000451608.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287
• Publications: 8 publications found

Genes affected

ENSG00000264324 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
NECAP1P2		n.74350270T>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000264324	ENST00000451608.2	n.*240-7733A>C		intron_variant	Intron 6 of 38	5		ENSP00000416453.2
NECAP1P2	ENST00000455668.1	n.202T>G		non_coding_transcript_exon_variant	Exon 1 of 2	6

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

African (AFR) AF: 0.118 AC: 68 AN: 576

American (AMR) AF: 0.0565 AC: 48 AN: 850

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 17 AN: 136

East Asian (EAS) AF: 0.520 AC: 555 AN: 1068

South Asian (SAS) AF: 0.175 AC: 112 AN: 640

European-Finnish (FIN) AF: 0.112 AC: 168 AN: 1494

Middle Eastern (MID) AF: 0.0833 AC: 1 AN: 12

European-Non Finnish (NFE) AF: 0.111 AC: 500 AN: 4512

Other (OTH) AF: 0.114 AC: 49 AN: 428

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

African (AFR) AF: 0.164 AC: 6826 AN: 41544

American (AMR) AF: 0.119 AC: 1821 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 473 AN: 3470

East Asian (EAS) AF: 0.473 AC: 2444 AN: 5170

South Asian (SAS) AF: 0.218 AC: 1053 AN: 4824

European-Finnish (FIN) AF: 0.108 AC: 1146 AN: 10610

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7663 AN: 68012

Other (OTH) AF: 0.148 AC: 312 AN: 2108

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
PhyloP100		0.29

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

Other links and lift over

dbSNP: rs7581836; hg19: chr2-74577397;