2-74785200-C-T

Variant names:

• chr2-74785200-C-T
• rs6546923
• ENST00000690069.1:n.457-20533C>T

Variant summary

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

The ENST00000690069.1(ENSG00000286739):​n.457-20533C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.701 in 152,020 control chromosomes in the GnomAD database, including 38,268 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 0.70 (38268 hom., cov: 31)
• Consequence: ENSG00000286739 ENST00000690069.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620

Genes affected

ENSG00000286739 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.843 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
ENSG00000286739	ENST00000690069.1	n.457-20533C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.701 AC: 106521 AN: 151902 Hom.: 38230 Cov.: 31

Gnomad AFR AF: 0.851

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.726

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.701 AC: 106600 AN: 152020 Hom.: 38268 Cov.: 31 AF XY: 0.701 AC XY: 52088 AN XY: 74320

Gnomad4 AFR AF: 0.851

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.669

Gnomad4 EAS AF: 0.454

Gnomad4 SAS AF: 0.580

Gnomad4 FIN AF: 0.726

Gnomad4 NFE AF: 0.643

Gnomad4 OTH AF: 0.661

Alfa AF: 0.646 Hom.: 65815

Bravo AF: 0.702

Asia WGS AF: 0.496 AC: 1724 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6546923; hg19: chr2-75012327;