1-244010570-C-A

Variant names:

• chr1-244010570-C-A
• rs10927101
• ENST00000440494.1:n.527-127C>A

Variant summary

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

The ENST00000440494.1(LINC02774):​n.527-127C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 152,050 control chromosomes in the GnomAD database, including 15,216 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 0.44 (15213 hom., cov: 33)
  • Exomes 𝑓: 0.60 (3 hom.)
• Consequence: LINC02774 ENST00000440494.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.323
• Publications: 12 publications found

Genes affected

LINC02774 (HGNC:27923): (long intergenic non-protein coding RNA 2774)

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 = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02774	NR_033883.1	n.527-127C>A		intron_variant	Intron 5 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02774	ENST00000440494.1	n.527-127C>A		intron_variant	Intron 5 of 11	1
LINC02774	ENST00000806746.1	n.118C>A		non_coding_transcript_exon_variant	Exon 1 of 5
LINC02774	ENST00000652928.1	n.259-127C>A		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66691 AN: 151922 Hom.: 15197 Cov.: 33

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.448

GnomAD4 exome AF: 0.600 AC: 6 AN: 10 Hom.: 3 AF XY: 0.600 AC XY: 6 AN XY: 10

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 4 AN: 8

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.439 AC: 66754 AN: 152040 Hom.: 15213 Cov.: 33 AF XY: 0.441 AC XY: 32748 AN XY: 74308

African (AFR) AF: 0.512 AC: 21207 AN: 41454

American (AMR) AF: 0.471 AC: 7197 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1319 AN: 3468

East Asian (EAS) AF: 0.682 AC: 3524 AN: 5170

South Asian (SAS) AF: 0.415 AC: 2000 AN: 4818

European-Finnish (FIN) AF: 0.399 AC: 4209 AN: 10550

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.379 AC: 25780 AN: 67976

Other (OTH) AF: 0.450 AC: 952 AN: 2114

Alfa AF: 0.398 Hom.: 45752

Bravo AF: 0.450

Asia WGS AF: 0.557 AC: 1935 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	1.0
DANN	Benign	0.46
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs10927101; hg19: chr1-244173872;