ENST00000440609.1:n.98+35058C>T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373831	XR_923759.3	n.72+35058C>T		intron_variant	Intron 1 of 3
LOC105373831	XR_923760.2	n.72+35058C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000225421	ENST00000440609.1	n.98+35058C>T		intron_variant	Intron 1 of 2	4

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 v4.3

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

Other links and lift over

dbSNP: rs11893063; hg19: chr2-199601925;