2-224042630-C-T

Variant names:

• chr2-224042630-C-T
• rs282254
• ENST00000848792.1:n.1081C>T

Variant summary

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

The ENST00000848792.1(ENSG00000310283):​n.1081C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 151,928 control chromosomes in the GnomAD database, including 16,979 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 0.44 (16979 hom., cov: 32)
• Consequence: ENSG00000310283 ENST00000848792.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290
• Publications: 5 publications found

Genes affected

ENSG00000310283 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124907991	XR_007088103.1	n.*138C>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310283	ENST00000848792.1	n.1081C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000310283	ENST00000848790.1	n.*138C>T		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67421 AN: 151812 Hom.: 16975 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.444 AC: 67433 AN: 151928 Hom.: 16979 Cov.: 32 AF XY: 0.449 AC XY: 33305 AN XY: 74256

African (AFR) AF: 0.193 AC: 8009 AN: 41418

American (AMR) AF: 0.519 AC: 7931 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.528 AC: 1832 AN: 3470

East Asian (EAS) AF: 0.300 AC: 1552 AN: 5168

South Asian (SAS) AF: 0.542 AC: 2611 AN: 4816

European-Finnish (FIN) AF: 0.599 AC: 6312 AN: 10530

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.555 AC: 37678 AN: 67940

Other (OTH) AF: 0.471 AC: 994 AN: 2110

Alfa AF: 0.525 Hom.: 10812

Bravo AF: 0.425

Asia WGS AF: 0.413 AC: 1437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	12
DANN	Benign	0.72
PhyloP100		0.029

Splicing

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

Other links and lift over

dbSNP: rs282254; hg19: chr2-224907347;