1-243978530-A-T

Position:

• chr1-243978530-A-T

Variant summary

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

The NR_033883.1(LINC02774):​n.235+11A>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 0.171 in 152,144 control chromosomes in the GnomAD database, including 2,453 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 0.17 (2453 hom., cov: 32)
  • Exomes 𝑓: 0.17 (0 hom.)
• Consequence: LINC02774 NR_033883.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.856

Genes affected

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

LOC105373258 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02774	NR_033883.1	n.235+11A>T		intron_variant, non_coding_transcript_variant
LOC105373258	XR_949337.2	n.211+774T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02774	ENST00000440494.1	n.235+11A>T		intron_variant, non_coding_transcript_variant		1
LINC02774	ENST00000652928.1	n.186+11A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25969 AN: 152022 Hom.: 2452 Cov.: 32

Gnomad AFR AF: 0.0993

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.0792

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.159

GnomAD4 exome AF: 0.167 AC: 1 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

Gnomad4 EAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.250

GnomAD4 genome AF: 0.171 AC: 25973 AN: 152138 Hom.: 2453 Cov.: 32 AF XY: 0.170 AC XY: 12653 AN XY: 74362

Gnomad4 AFR AF: 0.0991

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.0792

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.162

Alfa AF: 0.193 Hom.: 351

Bravo AF: 0.167

Asia WGS AF: 0.138 AC: 481 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	0.28
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2131817; hg19: chr1-244141832;