2-21600126-C-T

Variant names:

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

Variant summary

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

The ENST00000435237.1(ENSG00000231204):​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: ENSG00000231204 ENST00000435237.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13
• Publications: 5 publications found

Genes affected

ENSG00000231204 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435237.1. 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
	ENSG00000231204	ENST00000435237.1	TSL:3	n.193+70883C>T		intron	N/A
	ENSG00000231204	ENST00000717099.1		n.555+35060C>T		intron	N/A
	ENSG00000231204	ENST00000753412.1		n.73+70883C>T		intron	N/A

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

African (AFR) AF: 0.604 AC: 25033 AN: 41444

American (AMR) AF: 0.893 AC: 13647 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.962 AC: 3340 AN: 3472

East Asian (EAS) AF: 0.852 AC: 4407 AN: 5170

South Asian (SAS) AF: 0.954 AC: 4602 AN: 4826

European-Finnish (FIN) AF: 0.977 AC: 10378 AN: 10620

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.967 AC: 65795 AN: 68028

Other (OTH) AF: 0.869 AC: 1838 AN: 2114

Alfa AF: 0.938 Hom.: 104763

Bravo AF: 0.837

Asia WGS AF: 0.864 AC: 3007 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.75
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs1991126; hg19: chr2-21822998;