rs8134080

Variant names:

• chr21-28133086-G-A
• rs8134080
• ENST00000453420.5:n.706-13212C>T

Your query was ambiguous. Multiple possible variants found:

• chr21-28133086-G-A
• chr21-28133086-G-C

Variant summary

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

The ENST00000453420.5(LINC01695):​n.706-13212C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 152,012 control chromosomes in the GnomAD database, including 16,806 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 0.47 (16806 hom., cov: 32)
• Consequence: LINC01695 ENST00000453420.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530
• Publications: 2 publications found

Genes affected

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

LINC01697 (HGNC:52485): (long intergenic non-protein coding RNA 1697)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01697	NR_126010.1	n.438-2228G>A		intron_variant	Intron 3 of 4
LINC01695	NR_126012.1	n.706-13212C>T		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01695	ENST00000453420.5	n.706-13212C>T		intron_variant	Intron 5 of 5	1
LINC01697	ENST00000426534.2	n.448-2228G>A		intron_variant	Intron 3 of 4	2
LINC01697	ENST00000609782.1	n.505-2228G>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70762 AN: 151894 Hom.: 16774 Cov.: 32

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.391

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.466 AC: 70848 AN: 152012 Hom.: 16806 Cov.: 32 AF XY: 0.464 AC XY: 34457 AN XY: 74306

African (AFR) AF: 0.542 AC: 22456 AN: 41458

American (AMR) AF: 0.518 AC: 7911 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1645 AN: 3468

East Asian (EAS) AF: 0.338 AC: 1747 AN: 5168

South Asian (SAS) AF: 0.436 AC: 2102 AN: 4822

European-Finnish (FIN) AF: 0.385 AC: 4061 AN: 10560

Middle Eastern (MID) AF: 0.403 AC: 117 AN: 290

European-Non Finnish (NFE) AF: 0.435 AC: 29552 AN: 67962

Other (OTH) AF: 0.431 AC: 911 AN: 2114

Alfa AF: 0.460 Hom.: 6295

Bravo AF: 0.478

Asia WGS AF: 0.401 AC: 1399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.67
PhyloP100		-0.053

Splicing

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

Other links and lift over

dbSNP: rs8134080; hg19: chr21-29505405;