rs7599142

Variant names:

• chr2-162136981-C-T
• rs7599142
• ENST00000727531.1:n.103+16702C>T

Variant summary

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

The ENST00000727531.1(ENSG00000236841):​n.103+16702C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 151,346 control chromosomes in the GnomAD database, including 11,913 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 0.38 (11913 hom., cov: 32)
• Consequence: ENSG00000236841 ENST00000727531.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250
• Publications: 4 publications found

Genes affected

ENSG00000236841 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929532	NR_110255.1	n.92+22449C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000236841	ENST00000727531.1	n.103+16702C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58239 AN: 151230 Hom.: 11912 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.380

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.385 AC: 58265 AN: 151346 Hom.: 11913 Cov.: 32 AF XY: 0.391 AC XY: 28932 AN XY: 73918

African (AFR) AF: 0.264 AC: 10905 AN: 41366

American (AMR) AF: 0.369 AC: 5609 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1665 AN: 3466

East Asian (EAS) AF: 0.703 AC: 3630 AN: 5160

South Asian (SAS) AF: 0.528 AC: 2542 AN: 4810

European-Finnish (FIN) AF: 0.440 AC: 4585 AN: 10422

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.414 AC: 27956 AN: 67604

Other (OTH) AF: 0.385 AC: 809 AN: 2100

Alfa AF: 0.374 Hom.: 1366

Bravo AF: 0.375

Asia WGS AF: 0.549 AC: 1894 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.4
DANN	Benign	0.59
PhyloP100		0.025

Splicing

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

Other links and lift over

dbSNP: rs7599142; hg19: chr2-162993491;