rs433632

Positions:

• chr21-42600313-A-G

Variant summary

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

The ENST00000419628.2(LINC01671):​n.778T>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 0.734 in 151,920 control chromosomes in the GnomAD database, including 41,875 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 0.73 (41866 hom., cov: 33)
  • Exomes 𝑓: 0.81 (9 hom.)
• Consequence: LINC01671 ENST00000419628.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

Genes affected

LINC01671 (HGNC:52459): (long intergenic non-protein coding RNA 1671)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01671	NR_131192.1	n.779T>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01671	ENST00000419628.2	n.778T>C		non_coding_transcript_exon_variant	2/2	1

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111447 AN: 151776 Hom.: 41829 Cov.: 33

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.736

Gnomad OTH AF: 0.726

GnomAD4 exome AF: 0.808 AC: 21 AN: 26 Hom.: 9 Cov.: 0 AF XY: 0.778 AC XY: 14 AN XY: 18

Gnomad4 ASJ exome AF: 1.00

Gnomad4 FIN exome AF: 0.800

Gnomad4 NFE exome AF: 0.700

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.734 AC: 111547 AN: 151894 Hom.: 41866 Cov.: 33 AF XY: 0.727 AC XY: 53930 AN XY: 74226

Gnomad4 AFR AF: 0.802

Gnomad4 AMR AF: 0.794

Gnomad4 ASJ AF: 0.687

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.594

Gnomad4 FIN AF: 0.715

Gnomad4 NFE AF: 0.736

Gnomad4 OTH AF: 0.723

Alfa AF: 0.724 Hom.: 17453

Bravo AF: 0.744

Asia WGS AF: 0.445 AC: 1546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.51
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs433632; hg19: chr21-44020423;