rs2758259

chr6-63483202-C-T

Variant summary

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

The ENST00000701584.1(ENSG00000289911):n.134-39444G>A 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 0.536 in 151,972 control chromosomes in the GnomAD database, including 23,683 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 0.54 (23683 hom., cov: 31)
• Consequence: ENST00000701584.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LGSN	XM_047418866.1	c.-963-39444G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000701584.1	n.134-39444G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81386 AN: 151854 Hom.: 23628 Cov.: 31

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.536 AC: 81509 AN: 151972 Hom.: 23683 Cov.: 31 AF XY: 0.533 AC XY: 39544 AN XY: 74260

Gnomad4 AFR AF: 0.772

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.496

Alfa AF: 0.500 Hom.: 4154

Bravo AF: 0.558

Asia WGS AF: 0.452 AC: 1569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.7
Dann	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2758259; hg19: chr6-64193107;