2-59436771-C-T

Variant names:

• chr2-59436771-C-T
• rs10490056
• ENST00000412409.3:n.545+158034G>A

Variant summary

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

The ENST00000412409.3(ENSG00000233891):​n.545+158034G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0509 in 152,030 control chromosomes in the GnomAD database, including 277 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 0.051 (277 hom., cov: 32)
• Consequence: ENSG00000233891 ENST00000412409.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670
• Publications: 1 publications found

Genes affected

ENSG00000233891 (HGNC:58936):

ENSG00000231815 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000412409.3. 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
	ENSG00000233891	ENST00000412409.3	TSL:3	n.545+158034G>A		intron	N/A
	ENSG00000231815	ENST00000415159.1	TSL:3	n.151+1408C>T		intron	N/A
	ENSG00000233891	ENST00000606382.1	TSL:5	n.433+75238G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0509 AC: 7729 AN: 151912 Hom.: 273 Cov.: 32

Gnomad AFR AF: 0.0701

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0984

Gnomad ASJ AF: 0.0776

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.0290

Gnomad FIN AF: 0.0246

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0283

Gnomad OTH AF: 0.0641

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

GnomAD4 genome AF: 0.0509 AC: 7741 AN: 152030 Hom.: 277 Cov.: 32 AF XY: 0.0514 AC XY: 3817 AN XY: 74308

African (AFR) AF: 0.0700 AC: 2906 AN: 41496

American (AMR) AF: 0.0989 AC: 1507 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.0776 AC: 269 AN: 3468

East Asian (EAS) AF: 0.108 AC: 557 AN: 5140

South Asian (SAS) AF: 0.0293 AC: 141 AN: 4816

European-Finnish (FIN) AF: 0.0246 AC: 261 AN: 10594

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0283 AC: 1925 AN: 67964

Other (OTH) AF: 0.0643 AC: 136 AN: 2114

Alfa AF: 0.0278 Hom.: 15

Bravo AF: 0.0611

Asia WGS AF: 0.0630 AC: 221 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.0
DANN	Benign	0.72
PhyloP100		-0.067

Splicing

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

Other links and lift over

dbSNP: rs10490056; hg19: chr2-59663906;