rs10746414

Positions:

• chr1-221886008-A-G
• chr1-221886008-A-T

Variant summary

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

The XR_007066885.1(LOC124904517):​n.331-30070A>G 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 0.708 in 151,744 control chromosomes in the GnomAD database, including 38,493 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 0.71 (38493 hom., cov: 29)
• Consequence: LOC124904517 XR_007066885.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904517	XR_007066885.1	n.331-30070A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02257	ENST00000433576.5	n.328-2120T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.708 AC: 107355 AN: 151626 Hom.: 38444 Cov.: 29

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.701

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.708 AC: 107459 AN: 151744 Hom.: 38493 Cov.: 29 AF XY: 0.711 AC XY: 52711 AN XY: 74130

Gnomad4 AFR AF: 0.714

Gnomad4 AMR AF: 0.780

Gnomad4 ASJ AF: 0.680

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.642

Gnomad4 NFE AF: 0.676

Gnomad4 OTH AF: 0.694

Alfa AF: 0.692 Hom.: 14338

Bravo AF: 0.721

Asia WGS AF: 0.895 AC: 3109 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.20
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: rs10746414; hg19: chr1-222059350;