21-28133115-G-T

Position:

• chr21-28133115-G-T

Variant summary

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

The ENST00000453420.5(LINC01695):​n.706-13241C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,110 control chromosomes in the GnomAD database, including 1,789 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 0.14 (1789 hom., cov: 32)
• Consequence: LINC01695 ENST00000453420.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.175

Genes affected

LINC01695 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01697	NR_126010.1	n.438-2199G>T		intron_variant
LINC01695	NR_126012.1	n.706-13241C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01695	ENST00000453420.5	n.706-13241C>A		intron_variant		1
LINC01697	ENST00000426534.2	n.448-2199G>T		intron_variant		2
LINC01697	ENST00000609782.1	n.505-2199G>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20885 AN: 151992 Hom.: 1784 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.0813

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.0904

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.137 AC: 20899 AN: 152110 Hom.: 1789 Cov.: 32 AF XY: 0.140 AC XY: 10384 AN XY: 74348

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.459

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.0904

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.157

Alfa AF: 0.118 Hom.: 2434

Bravo AF: 0.141

Asia WGS AF: 0.287 AC: 995 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	2.1
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2831524; hg19: chr21-29505434;