rs9346455

Positions:

• chr6-71282113-T-G

Variant summary

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

The XR_007059640.1(LOC124901339):​n.7634A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,090 control chromosomes in the GnomAD database, including 1,656 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 0.13 (1656 hom., cov: 32)
• Consequence: LOC124901339 XR_007059640.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.683

Genes affected

LOC124901339 (HGNC:):

LINC00472 (HGNC:21380): (long intergenic non-protein coding RNA 472)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901339	XR_007059640.1	n.7634A>C		non_coding_transcript_exon_variant	5/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00472	ENST00000710850.1	n.355-48456A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20325 AN: 151972 Hom.: 1651 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.0912

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.0769

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.0829

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0858

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.134 AC: 20373 AN: 152090 Hom.: 1656 Cov.: 32 AF XY: 0.135 AC XY: 10075 AN XY: 74356

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.0769

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.0829

Gnomad4 NFE AF: 0.0858

Gnomad4 OTH AF: 0.148

Alfa AF: 0.103 Hom.: 272

Bravo AF: 0.147

Asia WGS AF: 0.223 AC: 772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.78
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9346455; hg19: chr6-71991816;