chr1-221892367-T-C

Position:

• chr1-221892367-T-C

Variant summary

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

The XR_007066885.1(LOC124904517):​n.331-23711T>C 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 0.466 in 151,992 control chromosomes in the GnomAD database, including 17,269 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 0.47 (17269 hom., cov: 32)
• Consequence: LOC124904517 XR_007066885.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.383

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904517	XR_007066885.1	n.331-23711T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02257	ENST00000433576.5	n.328-8479A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70762 AN: 151874 Hom.: 17256 Cov.: 32

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.466 AC: 70815 AN: 151992 Hom.: 17269 Cov.: 32 AF XY: 0.462 AC XY: 34293 AN XY: 74302

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.416

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.501

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.479

Alfa AF: 0.434 Hom.: 29352

Bravo AF: 0.465

Asia WGS AF: 0.382 AC: 1330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.89
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7547751; hg19: chr1-222065709;