rs2131817

Variant names:

• chr1-243978530-A-T
• rs2131817
• ENST00000440494.1:n.235+11A>T

Variant summary

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

The ENST00000440494.1(LINC02774):​n.235+11A>T variant causes a intron 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 ENST00000440494.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.856
• Publications: 1 publications found

Genes affected

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

LOC105373258 (HGNC:):

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02774	NR_033883.1	n.235+11A>T		intron_variant	Intron 2 of 11
LOC105373258	XR_949337.2	n.211+774T>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02774	ENST00000440494.1	n.235+11A>T		intron_variant	Intron 2 of 11	1
LINC02774	ENST00000806743.1	n.322A>T		non_coding_transcript_exon_variant	Exon 2 of 2
LINC02774	ENST00000652928.1	n.186+11A>T		intron_variant	Intron 2 of 5

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

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: 0.250 AC: 1 AN: 4

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.0991 AC: 4114 AN: 41512

American (AMR) AF: 0.200 AC: 3050 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 525 AN: 3470

East Asian (EAS) AF: 0.0792 AC: 410 AN: 5176

South Asian (SAS) AF: 0.181 AC: 872 AN: 4814

European-Finnish (FIN) AF: 0.195 AC: 2063 AN: 10582

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14405 AN: 67990

Other (OTH) AF: 0.162 AC: 342 AN: 2106

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
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs2131817; hg19: chr1-244141832;