rs914238

chr21-45595747-T-C

Variant summary

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

The NR_146912.1(LINC01694):n.56-644T>C 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 0.476 in 152,286 control chromosomes in the GnomAD database, including 17,320 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 0.48 (17299 hom., cov: 34)
  • Exomes 𝑓: 0.50 (21 hom.)
• Consequence: LINC01694 NR_146912.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.615

Genes affected

LINC01694 (HGNC:52481): (long intergenic non-protein coding RNA 1694)

LOC107985485 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01694	NR_146912.1	n.56-644T>C		intron_variant, non_coding_transcript_variant
LOC107985485	XR_001755092.2	n.200-5533A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01694	ENST00000441095.2	n.56-644T>C		intron_variant, non_coding_transcript_variant		3
LINC01694	ENST00000424569.1	n.120+86T>C		intron_variant, non_coding_transcript_variant		5
LINC01694	ENST00000662558.1	n.368+86T>C		intron_variant, non_coding_transcript_variant
LINC01694	ENST00000685333.1	n.187-644T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72276 AN: 152020 Hom.: 17274 Cov.: 34

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.485

GnomAD4 exome AF: 0.500 AC: 75 AN: 150 Hom.: 21 AF XY: 0.480 AC XY: 47 AN XY: 98

Gnomad4 AMR exome AF: 0.250

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.444

Gnomad4 NFE exome AF: 0.533

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.476 AC: 72349 AN: 152136 Hom.: 17299 Cov.: 34 AF XY: 0.478 AC XY: 35583 AN XY: 74374

Gnomad4 AFR AF: 0.454

Gnomad4 AMR AF: 0.466

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.577

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.485

Gnomad4 OTH AF: 0.491

Alfa AF: 0.489 Hom.: 30160

Bravo AF: 0.469

Asia WGS AF: 0.576 AC: 2001 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	4.1
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs914238; hg19: chr21-47015661;