rs6668395

Positions:

• chr1-221824262-G-A
• chr1-221824262-G-T

Variant summary

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

The ENST00000665303.1(LINC01655):​n.550+3300C>T 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 0.226 in 151,928 control chromosomes in the GnomAD database, including 4,705 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 0.23 (4705 hom., cov: 32)
• Consequence: LINC01655 ENST00000665303.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192

Genes affected

LINC01655 (HGNC:52443): (long intergenic non-protein coding RNA 1655)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01655	ENST00000665303.1	n.550+3300C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34348 AN: 151810 Hom.: 4701 Cov.: 32

Gnomad AFR AF: 0.0811

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.226 AC: 34354 AN: 151928 Hom.: 4705 Cov.: 32 AF XY: 0.228 AC XY: 16919 AN XY: 74234

Gnomad4 AFR AF: 0.0810

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.490

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.208

Alfa AF: 0.238 Hom.: 797

Bravo AF: 0.212

Asia WGS AF: 0.311 AC: 1080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.91
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6668395; hg19: chr1-221997604;