rs1440620

Positions:

• chr1-214088007-T-C

Variant summary

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

The ENST00000637598.1(LINC02775):​n.662-15569A>G 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 0.283 in 152,098 control chromosomes in the GnomAD database, including 6,940 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 0.28 (6940 hom., cov: 32)
• Consequence: LINC02775 ENST00000637598.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550

Genes affected

LINC02775 (HGNC:54294): (long intergenic non-protein coding RNA 2775)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02775	XR_922584.2	n.261-15569A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02775	ENST00000637598.1	n.662-15569A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43112 AN: 151980 Hom.: 6941 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.283 AC: 43117 AN: 152098 Hom.: 6940 Cov.: 32 AF XY: 0.286 AC XY: 21250 AN XY: 74330

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.280

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.282

Alfa AF: 0.311 Hom.: 2802

Bravo AF: 0.268

Asia WGS AF: 0.328 AC: 1143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.99
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1440620; hg19: chr1-214261350;