rs6516819

Variant names:

• chr21-28138574-T-G
• rs6516819
• ENST00000453420.5:n.706-18700A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000453420.5(LINC01695):​n.706-18700A>C variant causes a intron 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 ENST00000453420.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.592
• Publications: 7 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC01695	NR_126012.1	n.706-18700A>C		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01695	ENST00000453420.5	n.706-18700A>C		intron_variant	Intron 5 of 5	1
LINC01695	ENST00000737222.1	n.192-14720A>C		intron_variant	Intron 2 of 2
LINC01695	ENST00000737223.1	n.355-14720A>C		intron_variant	Intron 3 of 3
LINC01695	ENST00000737224.1	n.260-14720A>C		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.571 AC: 23646 AN: 41408

American (AMR) AF: 0.558 AC: 8516 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.582 AC: 2019 AN: 3468

East Asian (EAS) AF: 0.340 AC: 1751 AN: 5154

South Asian (SAS) AF: 0.519 AC: 2494 AN: 4804

European-Finnish (FIN) AF: 0.434 AC: 4574 AN: 10550

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.493 AC: 33487 AN: 67962

Other (OTH) AF: 0.493 AC: 1039 AN: 2108

Alfa AF: 0.505 Hom.: 29029

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
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs6516819; hg19: chr21-29510893;