chr2-142137004-C-A

Variant names:

• chr2-142137004-C-A
• rs10194564
• ENST00000436132.1:n.67+760G>T

Variant summary

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

The ENST00000436132.1(ENSG00000244125):​n.67+760G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,134 control chromosomes in the GnomAD database, including 1,307 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 0.12 (1307 hom., cov: 32)
• Consequence: ENSG00000244125 ENST00000436132.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388
• Publications: 3 publications found

Genes affected

ENSG00000244125 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000244125	ENST00000436132.1	n.67+760G>T		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18388 AN: 152016 Hom.: 1309 Cov.: 32

Gnomad AFR AF: 0.0763

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.0884

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.0116

Gnomad SAS AF: 0.0778

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.121 AC: 18391 AN: 152134 Hom.: 1307 Cov.: 32 AF XY: 0.119 AC XY: 8846 AN XY: 74384

African (AFR) AF: 0.0763 AC: 3167 AN: 41522

American (AMR) AF: 0.0883 AC: 1349 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 936 AN: 3470

East Asian (EAS) AF: 0.0114 AC: 59 AN: 5182

South Asian (SAS) AF: 0.0770 AC: 371 AN: 4816

European-Finnish (FIN) AF: 0.184 AC: 1948 AN: 10564

Middle Eastern (MID) AF: 0.140 AC: 41 AN: 292

European-Non Finnish (NFE) AF: 0.148 AC: 10084 AN: 67982

Other (OTH) AF: 0.125 AC: 265 AN: 2116

Alfa AF: 0.128 Hom.: 1094

Bravo AF: 0.113

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.45
DANN	Benign	0.36
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs10194564; hg19: chr2-142894573;