rs4335625

chr12-131215867-G-T

Variant summary

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

The ENST00000536191.2(LINC01257):n.1463+5472G>T 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 0.393 in 151,930 control chromosomes in the GnomAD database, including 12,021 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 0.39 (12021 hom., cov: 32)
• Consequence: LINC01257 ENST00000536191.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

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=-1.25).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01257	ENST00000536191.2	n.1463+5472G>T		intron_variant, non_coding_transcript_variant		4
LINC01257	ENST00000653253.1	n.1312-979G>T		intron_variant, non_coding_transcript_variant
LINC01257	ENST00000654133.1	n.1620+319G>T		intron_variant, non_coding_transcript_variant
LINC01257	ENST00000668353.1	n.1517-979G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59590 AN: 151812 Hom.: 11992 Cov.: 32

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.393 AC: 59680 AN: 151930 Hom.: 12021 Cov.: 32 AF XY: 0.403 AC XY: 29946 AN XY: 74244

Gnomad4 AFR AF: 0.361

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.574

Gnomad4 SAS AF: 0.603

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.369

Alfa AF: 0.390 Hom.: 1825

Bravo AF: 0.385

Asia WGS AF: 0.567 AC: 1969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.3
Cadd	Benign	0.20
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4335625; hg19: chr12-131700412;