rs1358379

chr6-71403739-T-C

Variant summary

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

The ENST00000710850.1(LINC00472):n.354+12671A>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 0.0488 in 350,218 control chromosomes in the GnomAD database, including 559 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 0.060 (319 hom., cov: 32)
  • Exomes 𝑓: 0.040 (240 hom.)
• Consequence: LINC00472 ENST00000710850.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.255

Genes affected

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0988 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00472	ENST00000710850.1	n.354+12671A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0596 AC: 9074 AN: 152128 Hom.: 318 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0307

Gnomad ASJ AF: 0.0493

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0213

Gnomad FIN AF: 0.0488

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0508

Gnomad OTH AF: 0.0540

GnomAD4 exome AF: 0.0404 AC: 7991 AN: 197972 Hom.: 240 AF XY: 0.0381 AC XY: 4144 AN XY: 108902

Gnomad4 AFR exome AF: 0.0926

Gnomad4 AMR exome AF: 0.0218

Gnomad4 ASJ exome AF: 0.0368

Gnomad4 EAS exome AF: 0.000274

Gnomad4 SAS exome AF: 0.0238

Gnomad4 FIN exome AF: 0.0489

Gnomad4 NFE exome AF: 0.0475

Gnomad4 OTH exome AF: 0.0434

GnomAD4 genome AF: 0.0597 AC: 9083 AN: 152246 Hom.: 319 Cov.: 32 AF XY: 0.0585 AC XY: 4352 AN XY: 74442

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.0307

Gnomad4 ASJ AF: 0.0493

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0213

Gnomad4 FIN AF: 0.0488

Gnomad4 NFE AF: 0.0508

Gnomad4 OTH AF: 0.0535

Alfa AF: 0.0557 Hom.: 29

Bravo AF: 0.0602

Asia WGS AF: 0.0140 AC: 50 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.7
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1358379; hg19: chr6-72113442;