rs4129271

chr1-221896278-G-Achr1-221896278-G-C

Variant summary

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

The XR_007066885.1(LOC124904517):n.331-19800G>A 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 0.247 in 151,950 control chromosomes in the GnomAD database, including 5,083 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 0.25 (5083 hom., cov: 32)
• Consequence: LOC124904517 XR_007066885.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.271

Genes affected

LOC124904517 (HGNC:):

LINC02257 (HGNC:53159): (long intergenic non-protein coding RNA 2257)

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 (NFE) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904517	XR_007066885.1	n.331-19800G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02257	ENST00000433576.5	n.328-12390C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37465 AN: 151830 Hom.: 5080 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.247 AC: 37472 AN: 151950 Hom.: 5083 Cov.: 32 AF XY: 0.245 AC XY: 18210 AN XY: 74270

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.199

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: 0.259

Alfa AF: 0.269 Hom.: 750

Bravo AF: 0.232

Asia WGS AF: 0.0900 AC: 316 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	6.2
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4129271; hg19: chr1-222069620;