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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000451608.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000264324	ENST00000451608.2	TSL:5	n.*240-7733A>C		intron	N/A	ENSP00000416453.2	E7EWF7
	NECAP1P2	ENST00000455668.1	TSL:6	n.202T>G		non_coding_transcript_exon	Exon 1 of 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

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7581836;

hg19: chr2-74577397;