chr2-59714731-A-C

Variant names:

• chr2-59714731-A-C
• rs155563
• ENST00000412409.3:n.261+4845T>G

Variant summary

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

The ENST00000412409.3(ENSG00000233891):​n.261+4845T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 151,770 control chromosomes in the GnomAD database, including 18,637 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 0.48 (18637 hom., cov: 31)
• Consequence: ENSG00000233891 ENST00000412409.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.839
• Publications: 1 publications found

Genes affected

ENSG00000233891 (HGNC:58936):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.728 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.261+4845T>G		intron	N/A
	ENSG00000233891	ENST00000435557.1	TSL:4	n.114+18487T>G		intron	N/A
	ENSG00000233891	ENST00000606382.1	TSL:5	n.236+112415T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73536 AN: 151652 Hom.: 18619 Cov.: 31

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.572

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.485 AC: 73590 AN: 151770 Hom.: 18637 Cov.: 31 AF XY: 0.485 AC XY: 35937 AN XY: 74156

African (AFR) AF: 0.602 AC: 24953 AN: 41428

American (AMR) AF: 0.416 AC: 6330 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1277 AN: 3468

East Asian (EAS) AF: 0.747 AC: 3833 AN: 5128

South Asian (SAS) AF: 0.444 AC: 2131 AN: 4802

European-Finnish (FIN) AF: 0.421 AC: 4432 AN: 10536

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.428 AC: 29034 AN: 67886

Other (OTH) AF: 0.464 AC: 976 AN: 2104

Alfa AF: 0.455 Hom.: 1967

Bravo AF: 0.489

Asia WGS AF: 0.506 AC: 1759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.37
DANN	Benign	0.48
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs155563; hg19: chr2-59941866;