rs11893063

Variant names:

• chr2-198737201-G-A
• rs11893063
• ENST00000440609.1:n.98+35058C>T

Variant summary

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

The ENST00000440609.1(ENSG00000225421):​n.98+35058C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 150,896 control chromosomes in the GnomAD database, including 12,038 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 0.37 (12038 hom., cov: 29)
• Consequence: ENSG00000225421 ENST00000440609.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370
• Publications: 8 publications found

Genes affected

ENSG00000225421 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000440609.1. 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
	ENSG00000225421	ENST00000440609.1	TSL:4	n.98+35058C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.370 AC: 55763 AN: 150798 Hom.: 12043 Cov.: 29

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.370 AC: 55771 AN: 150896 Hom.: 12038 Cov.: 29 AF XY: 0.376 AC XY: 27685 AN XY: 73610

African (AFR) AF: 0.140 AC: 5748 AN: 41008

American (AMR) AF: 0.432 AC: 6536 AN: 15140

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1760 AN: 3470

East Asian (EAS) AF: 0.377 AC: 1926 AN: 5104

South Asian (SAS) AF: 0.279 AC: 1332 AN: 4778

European-Finnish (FIN) AF: 0.587 AC: 6034 AN: 10284

Middle Eastern (MID) AF: 0.418 AC: 122 AN: 292

European-Non Finnish (NFE) AF: 0.460 AC: 31182 AN: 67820

Other (OTH) AF: 0.379 AC: 793 AN: 2094

Alfa AF: 0.424 Hom.: 18406

Bravo AF: 0.343

Asia WGS AF: 0.324 AC: 1127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.6
DANN	Benign	0.54
PhyloP100		0.037

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11893063;

hg19: chr2-199601925;