2-21600126-C-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, non coding transcript 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: ENST00000435237.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000435237.1	n.193+70883C>T		intron_variant, non_coding_transcript_variant		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;