rs4335625

Variant names:

• chr12-131215867-G-T
• rs4335625
• ENST00000536191.2:n.1463+5472G>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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01257	ENST00000536191.2	n.1463+5472G>T		intron_variant	Intron 3 of 3	4
LINC01257	ENST00000653253.1	n.1312-979G>T		intron_variant	Intron 2 of 2
LINC01257	ENST00000654133.1	n.1620+319G>T		intron_variant	Intron 4 of 4
LINC01257	ENST00000668353.1	n.1517-979G>T		intron_variant	Intron 3 of 3

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;