rs9346455

Variant names:

• chr6-71282113-T-G
• rs9346455
• XR_007059633.1:n.2594A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007059633.1(LOC124901339):​n.2594A>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_007059633.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.683
• Publications: 6 publications found

Genes affected

LOC124901339 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC124901339	XR_007059633.1	n.2594A>C		non_coding_transcript_exon_variant	Exon 5 of 6
LOC124901339	XR_007059637.1	n.5249A>C		non_coding_transcript_exon_variant	Exon 5 of 5
LOC124901339	XR_007059638.1	n.4458A>C		non_coding_transcript_exon_variant	Exon 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00472	ENST00000412751.5	n.106-4799A>C		intron_variant	Intron 2 of 3	3
LINC00472	ENST00000423255.5	n.126+2747A>C		intron_variant	Intron 2 of 2	3
LINC00472	ENST00000586232.5	n.525+1661A>C		intron_variant	Intron 6 of 7	5

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

African (AFR) AF: 0.198 AC: 8209 AN: 41436

American (AMR) AF: 0.188 AC: 2879 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0769 AC: 267 AN: 3470

East Asian (EAS) AF: 0.244 AC: 1262 AN: 5168

South Asian (SAS) AF: 0.128 AC: 614 AN: 4810

European-Finnish (FIN) AF: 0.0829 AC: 879 AN: 10602

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0858 AC: 5835 AN: 67990

Other (OTH) AF: 0.148 AC: 312 AN: 2114

Alfa AF: 0.121 Hom.: 854

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
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs9346455; hg19: chr6-71991816;