rs6516819

Positions:

• chr21-28138574-T-G

Variant summary

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

The NR_126012.1(LINC01695):​n.706-18700A>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 0.515 in 151,910 control chromosomes in the GnomAD database, including 20,414 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 0.52 (20414 hom., cov: 32)
• Consequence: LINC01695 NR_126012.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.592

Genes affected

LINC01695 (HGNC:52483): (long intergenic non-protein coding RNA 1695)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01695	NR_126012.1	n.706-18700A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01695	ENST00000453420.5	n.706-18700A>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78164 AN: 151792 Hom.: 20377 Cov.: 32

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.515 AC: 78255 AN: 151910 Hom.: 20414 Cov.: 32 AF XY: 0.512 AC XY: 38018 AN XY: 74248

Gnomad4 AFR AF: 0.571

Gnomad4 AMR AF: 0.558

Gnomad4 ASJ AF: 0.582

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.519

Gnomad4 FIN AF: 0.434

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.493

Alfa AF: 0.504 Hom.: 24929

Bravo AF: 0.526

Asia WGS AF: 0.438 AC: 1526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.6
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6516819; hg19: chr21-29510893;