rs224241

chr16-3267036-A-G

Variant summary

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

The ENST00000703449.1(ENSG00000290183):c.-171+3153A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,168 control chromosomes in the GnomAD database, including 3,650 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 0.20 (3650 hom., cov: 32)
  • Exomes 𝑓: 0.38 (0 hom.)
• Consequence: ENST00000703449.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.563

Genes affected

(HGNC:):

LINC00921 (HGNC:26830): (long intergenic non-protein coding RNA 921)

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 (AMR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00921	NR_033904.1	n.2002-90A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000703449.1	c.-171+3153A>G		intron_variant				P1
LINC00921	ENST00000706009.1	n.71-90A>G		intron_variant, non_coding_transcript_variant
LINC00921	ENST00000572123.4	n.188-90A>G		intron_variant, non_coding_transcript_variant		5
LINC00921	ENST00000573951.1	n.2027-90A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30160 AN: 152042 Hom.: 3651 Cov.: 32

Gnomad AFR AF: 0.0792

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.0387

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.210

GnomAD4 exome AF: 0.375 AC: 3 AN: 8 Hom.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

Gnomad4 NFE exome AF: 0.333

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.198 AC: 30157 AN: 152160 Hom.: 3650 Cov.: 32 AF XY: 0.201 AC XY: 14945 AN XY: 74384

Gnomad4 AFR AF: 0.0790

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.0387

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.207

Alfa AF: 0.234 Hom.: 595

Bravo AF: 0.196

Asia WGS AF: 0.0880 AC: 310 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	1.8
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs224241; hg19: chr16-3317036;