1-221896824-C-T

Position:

• chr1-221896824-C-T

Variant summary

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

The ENST00000433576.5(LINC02257):​n.328-12936G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 151,928 control chromosomes in the GnomAD database, including 5,424 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 0.26 (5424 hom., cov: 33)
• Consequence: LINC02257 ENST00000433576.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235

Genes affected

LINC02257 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904517	XR_007066885.1	n.331-19254C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02257	ENST00000433576.5	n.328-12936G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39087 AN: 151810 Hom.: 5421 Cov.: 33

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.257 AC: 39097 AN: 151928 Hom.: 5424 Cov.: 33 AF XY: 0.256 AC XY: 18984 AN XY: 74232

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.240

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.268

Alfa AF: 0.227 Hom.: 949

Bravo AF: 0.244

Asia WGS AF: 0.0950 AC: 331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12738322; hg19: chr1-222070166;