2-21600126-C-T

Variant names:

• chr2-21600126-C-T
• rs1991126
• ENST00000435237.1:n.193+70883C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000435237.1(ENSG00000233005):​n.193+70883C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.856 in 152,154 control chromosomes in the GnomAD database, including 57,704 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 0.86 (57704 hom., cov: 33)
• Consequence: ENSG00000233005 ENST00000435237.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13

Genes affected

ENSG00000233005 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.961 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
ENSG00000233005	ENST00000435237.1	n.193+70883C>T		intron_variant	Intron 3 of 5	3

Frequencies

GnomAD3 genomes AF: 0.856 AC: 130164 AN: 152036 Hom.: 57685 Cov.: 33

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.993

Gnomad AMR AF: 0.893

Gnomad ASJ AF: 0.962

Gnomad EAS AF: 0.852

Gnomad SAS AF: 0.953

Gnomad FIN AF: 0.977

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.967

Gnomad OTH AF: 0.869

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

GnomAD4 genome AF: 0.856 AC: 130220 AN: 152154 Hom.: 57704 Cov.: 33 AF XY: 0.858 AC XY: 63859 AN XY: 74394

Gnomad4 AFR AF: 0.604

Gnomad4 AMR AF: 0.893

Gnomad4 ASJ AF: 0.962

Gnomad4 EAS AF: 0.852

Gnomad4 SAS AF: 0.954

Gnomad4 FIN AF: 0.977

Gnomad4 NFE AF: 0.967

Gnomad4 OTH AF: 0.869

Alfa AF: 0.951 Hom.: 83344

Bravo AF: 0.837

Asia WGS AF: 0.864 AC: 3007 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1991126; hg19: chr2-21822998;