1-221899656-A-G

Variant names:

• chr1-221899656-A-G
• rs4846734
• ENST00000433576.5:n.327+14106T>C

Variant summary

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

The ENST00000433576.5(LINC02257):​n.327+14106T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,188 control chromosomes in the GnomAD database, including 3,796 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 0.22 (3796 hom., cov: 32)
• Consequence: LINC02257 ENST00000433576.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.663

Genes affected

LINC02257 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904517	XR_007066885.1	n.331-16422A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02257	ENST00000433576.5	n.327+14106T>C		intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.217 AC: 33002 AN: 152070 Hom.: 3798 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.217 AC: 33012 AN: 152188 Hom.: 3796 Cov.: 32 AF XY: 0.215 AC XY: 16030 AN XY: 74416

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.217

Alfa AF: 0.228 Hom.: 6007

Bravo AF: 0.222

Asia WGS AF: 0.233 AC: 810 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.67
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4846734; hg19: chr1-222072998;