rs155563

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000233891 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000233891	ENST00000412409.3	n.261+4845T>G		intron_variant	Intron 2 of 4	3
ENSG00000233891	ENST00000435557.1	n.114+18487T>G		intron_variant	Intron 1 of 2	4
ENSG00000271955	ENST00000606382.1	n.236+112415T>G		intron_variant	Intron 2 of 3	5

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

Gnomad4 AFR AF: 0.602

Gnomad4 AMR AF: 0.416

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.747

Gnomad4 SAS AF: 0.444

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.464

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs155563; hg19: chr2-59941866;