rs155563

chr2-59714731-A-C

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, non coding transcript 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: ENST00000412409.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.839

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000412409.3	n.261+4845T>G		intron_variant, non_coding_transcript_variant		3
	ENST00000606382.1	n.236+112415T>G		intron_variant, non_coding_transcript_variant		5
	ENST00000435557.1	n.114+18487T>G		intron_variant, non_coding_transcript_variant		4

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;