rs6668395

Variant names:

• chr1-221824262-G-A
• rs6668395
• ENST00000665303.1:n.550+3300C>T

Your query was ambiguous. Multiple possible variants found:

• 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 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192

Genes affected

LINC01655 (HGNC:):

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01655	ENST00000665303.1	n.550+3300C>T		intron_variant	Intron 4 of 4

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;