rs2451241

chr6-159100096-C-T

Variant summary

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

The XM_047419645.1(LOC112267968):c.153-4197G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 151,814 control chromosomes in the GnomAD database, including 11,289 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 (11289 hom., cov: 30)
• Consequence: LOC112267968 XM_047419645.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71

Genes affected

LOC112267968 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC112267968	XM_047419645.1	c.153-4197G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000642586.1	n.412+5592C>T		intron_variant, non_coding_transcript_variant
	ENST00000642829.1	n.330-4197G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57460 AN: 151696 Hom.: 11284 Cov.: 30

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.379 AC: 57470 AN: 151814 Hom.: 11289 Cov.: 30 AF XY: 0.378 AC XY: 28021 AN XY: 74174

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.237

Gnomad4 SAS AF: 0.436

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.388

Alfa AF: 0.419 Hom.: 18492

Bravo AF: 0.359

Asia WGS AF: 0.393 AC: 1371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.039
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2451241; hg19: chr6-159521128; COSMIC: COSV55964990;