rs7980440

Positions:

• chr12-131204527-G-C

Variant summary

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

The NR_026670.2(LINC01257):​n.372+1605G>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 0.381 in 151,954 control chromosomes in the GnomAD database, including 11,510 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 0.38 (11510 hom., cov: 31)
• Consequence: LINC01257 NR_026670.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780

Genes affected

LINC01257 (HGNC:26972): (long intergenic non-protein coding RNA 1257)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.22).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01257	NR_026670.2	n.372+1605G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01257	ENST00000376678.6	n.372+1605G>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57847 AN: 151834 Hom.: 11515 Cov.: 31

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.381 AC: 57850 AN: 151954 Hom.: 11510 Cov.: 31 AF XY: 0.375 AC XY: 27823 AN XY: 74256

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.348

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.390

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.403

Alfa AF: 0.414 Hom.: 1659

Bravo AF: 0.378

Asia WGS AF: 0.311 AC: 1083 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.2
CADD	Benign	1.2
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7980440; hg19: chr12-131689072;