chr1-38136401-C-A

Variant names:

• chr1-38136401-C-A
• rs7547921
• ENST00000641212.1:n.121G>T

Variant summary

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

The ENST00000641212.1(LINC02786):​n.121G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,262 control chromosomes in the GnomAD database, including 949 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 0.11 (949 hom., cov: 32)
  • Exomes 𝑓: 0.12 (0 hom.)
• Consequence: LINC02786 ENST00000641212.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30
• Publications: 11 publications found

Genes affected

LINC02786 (HGNC:54307): (long intergenic non-protein coding RNA 2786)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02786	XR_001737991.3	n.132G>T		non_coding_transcript_exon_variant	Exon 2 of 6
LINC02786	XR_007065917.1	n.132G>T		non_coding_transcript_exon_variant	Exon 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02786	ENST00000641212.1	n.121G>T		non_coding_transcript_exon_variant	Exon 2 of 5
LINC02786	ENST00000761499.1	n.155G>T		non_coding_transcript_exon_variant	Exon 2 of 4
LINC02786	ENST00000761500.1	n.278G>T		non_coding_transcript_exon_variant	Exon 3 of 3
LINC02786	ENST00000761510.1	n.306G>T		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16316 AN: 152102 Hom.: 949 Cov.: 32

Gnomad AFR AF: 0.0896

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.0934

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.0774

Gnomad FIN AF: 0.0993

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.111

GnomAD4 exome AF: 0.119 AC: 5 AN: 42 Hom.: 0 Cov.: 0 AF XY: 0.0714 AC XY: 2 AN XY: 28

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 3 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0625 AC: 2 AN: 32

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.107 AC: 16325 AN: 152220 Hom.: 949 Cov.: 32 AF XY: 0.109 AC XY: 8094 AN XY: 74424

African (AFR) AF: 0.0895 AC: 3717 AN: 41546

American (AMR) AF: 0.172 AC: 2622 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0934 AC: 324 AN: 3468

East Asian (EAS) AF: 0.179 AC: 924 AN: 5150

South Asian (SAS) AF: 0.0781 AC: 377 AN: 4826

European-Finnish (FIN) AF: 0.0993 AC: 1054 AN: 10616

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6917 AN: 68012

Other (OTH) AF: 0.110 AC: 233 AN: 2112

Alfa AF: 0.105 Hom.: 1801

Bravo AF: 0.114

Asia WGS AF: 0.106 AC: 370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	18
DANN	Benign	0.66
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs7547921; hg19: chr1-38602073;