rs2295956

Positions:

• chr6-71327573-A-C

Variant summary

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

The ENST00000710850.1(LINC00472):​n.354+88837T>G 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 0.219 in 152,140 control chromosomes in the GnomAD database, including 3,909 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 0.22 (3909 hom., cov: 33)
• Consequence: LINC00472 ENST00000710850.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.481

Genes affected

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

LOC124901339 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901339	XR_007059640.1	n.5610+2898T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00472	ENST00000710850.1	n.354+88837T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33374 AN: 152022 Hom.: 3907 Cov.: 33

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.0637

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.219 AC: 33394 AN: 152140 Hom.: 3909 Cov.: 33 AF XY: 0.212 AC XY: 15776 AN XY: 74386

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.0639

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.247

Alfa AF: 0.237 Hom.: 6500

Bravo AF: 0.226

Asia WGS AF: 0.111 AC: 389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.8
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2295956; hg19: chr6-72037276;