rs11701162

chr21-42606033-C-Achr21-42606033-C-G

Variant summary

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

The NR_131192.1(LINC01671):n.244-5185G>T 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 0.274 in 152,100 control chromosomes in the GnomAD database, including 5,836 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 0.27 (5836 hom., cov: 32)
• Consequence: LINC01671 NR_131192.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01671	NR_131192.1	n.244-5185G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01671	ENST00000419628.2	n.243-5185G>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41677 AN: 151982 Hom.: 5831 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.274 AC: 41705 AN: 152100 Hom.: 5836 Cov.: 32 AF XY: 0.272 AC XY: 20185 AN XY: 74342

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.288

Alfa AF: 0.275 Hom.: 8050

Bravo AF: 0.276

Asia WGS AF: 0.307 AC: 1068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.6
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11701162; hg19: chr21-44026143;