1-214088007-T-C

Variant names:

• chr1-214088007-T-C
• rs1440620
• ENST00000637598.1:n.662-15569A>G

Variant summary

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

The ENST00000729802.1(LINC02775):​n.85-15569A>G variant causes a intron 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 ENST00000729802.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000729802.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02775	ENST00000637598.1	TSL:5	n.662-15569A>G		intron	N/A
	LINC02775	ENST00000729802.1		n.85-15569A>G		intron	N/A
	LINC02775	ENST00000729803.1		n.364-15569A>G		intron	N/A

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

African (AFR) AF: 0.128 AC: 5323 AN: 41540

American (AMR) AF: 0.280 AC: 4282 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1016 AN: 3468

East Asian (EAS) AF: 0.371 AC: 1911 AN: 5150

South Asian (SAS) AF: 0.360 AC: 1734 AN: 4822

European-Finnish (FIN) AF: 0.384 AC: 4052 AN: 10562

Middle Eastern (MID) AF: 0.195 AC: 57 AN: 292

European-Non Finnish (NFE) AF: 0.352 AC: 23909 AN: 67952

Other (OTH) AF: 0.282 AC: 595 AN: 2110

Alfa AF: 0.320 Hom.: 16307

Bravo AF: 0.268

Asia WGS AF: 0.328 AC: 1143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.99
DANN	Benign	0.83
PhyloP100		-0.055

Splicing

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

Other links and lift over

dbSNP: rs1440620; hg19: chr1-214261350;