2-136132489-C-T

Variant names:

• chr2-136132489-C-T
• rs7574456
• ENST00000805101.1:n.685+5039C>T

Variant summary

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

The ENST00000805101.1(ENSG00000304642):​n.685+5039C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.703 in 151,850 control chromosomes in the GnomAD database, including 39,077 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 0.70 (39077 hom., cov: 30)
• Consequence: ENSG00000304642 ENST00000805101.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119
• Publications: 2 publications found

Genes affected

ENSG00000304642 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 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
ENSG00000304642	ENST00000805101.1	n.685+5039C>T		intron_variant	Intron 1 of 1
ENSG00000304642	ENST00000805102.1	n.141+5039C>T		intron_variant	Intron 1 of 1
ENSG00000304710	ENST00000805738.1	n.-102C>T		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.703 AC: 106640 AN: 151732 Hom.: 39072 Cov.: 30

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.858

Gnomad EAS AF: 0.969

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.872

Gnomad MID AF: 0.876

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.703 AC: 106687 AN: 151850 Hom.: 39077 Cov.: 30 AF XY: 0.710 AC XY: 52672 AN XY: 74196

African (AFR) AF: 0.494 AC: 20407 AN: 41350

American (AMR) AF: 0.715 AC: 10916 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.858 AC: 2973 AN: 3464

East Asian (EAS) AF: 0.969 AC: 4996 AN: 5158

South Asian (SAS) AF: 0.721 AC: 3462 AN: 4802

European-Finnish (FIN) AF: 0.872 AC: 9225 AN: 10576

Middle Eastern (MID) AF: 0.866 AC: 253 AN: 292

European-Non Finnish (NFE) AF: 0.769 AC: 52244 AN: 67922

Other (OTH) AF: 0.736 AC: 1550 AN: 2106

Alfa AF: 0.746 Hom.: 5200

Bravo AF: 0.683

Asia WGS AF: 0.826 AC: 2874 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	9.1
DANN	Benign	0.79
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs7574456; hg19: chr2-136890059;