7-108883946-T-G

Variant names:

• chr7-108883946-T-G
• rs2280645
• ENST00000624695.1:n.*29A>C

Variant summary

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

The ENST00000624695.1(LINC02903):​n.*29A>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0776 in 1,326,880 control chromosomes in the GnomAD database, including 4,308 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 0.064 (369 hom., cov: 31)
  • Exomes 𝑓: 0.079 (3939 hom.)
• Consequence: LINC02903 ENST00000624695.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206
• Publications: 3 publications found

Genes affected

LINC02903 (HGNC:33712): (long intergenic non-protein coding RNA 2903)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0892 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02903	NR_171002.1	n.*29A>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02903	ENST00000624695.1	n.*29A>C		downstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.0645 AC: 9813 AN: 152186 Hom.: 370 Cov.: 31

Gnomad AFR AF: 0.0216

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0483

Gnomad ASJ AF: 0.0718

Gnomad EAS AF: 0.0968

Gnomad SAS AF: 0.0732

Gnomad FIN AF: 0.0961

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0854

Gnomad OTH AF: 0.0630

GnomAD4 exome AF: 0.0794 AC: 93203 AN: 1174576 Hom.: 3939 Cov.: 22 AF XY: 0.0788 AC XY: 45866 AN XY: 582174

African (AFR) AF: 0.0186 AC: 473 AN: 25390

American (AMR) AF: 0.0431 AC: 1556 AN: 36070

Ashkenazi Jewish (ASJ) AF: 0.0727 AC: 1152 AN: 15856

East Asian (EAS) AF: 0.110 AC: 1820 AN: 16566

South Asian (SAS) AF: 0.0663 AC: 5343 AN: 80540

European-Finnish (FIN) AF: 0.0913 AC: 2231 AN: 24436

Middle Eastern (MID) AF: 0.0619 AC: 232 AN: 3750

European-Non Finnish (NFE) AF: 0.0830 AC: 77160 AN: 929286

Other (OTH) AF: 0.0758 AC: 3236 AN: 42682

GnomAD4 genome AF: 0.0644 AC: 9814 AN: 152304 Hom.: 369 Cov.: 31 AF XY: 0.0658 AC XY: 4898 AN XY: 74466

African (AFR) AF: 0.0216 AC: 898 AN: 41584

American (AMR) AF: 0.0485 AC: 742 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0718 AC: 249 AN: 3470

East Asian (EAS) AF: 0.0962 AC: 499 AN: 5186

South Asian (SAS) AF: 0.0733 AC: 354 AN: 4830

European-Finnish (FIN) AF: 0.0961 AC: 1019 AN: 10602

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0854 AC: 5810 AN: 68016

Other (OTH) AF: 0.0633 AC: 134 AN: 2116

Alfa AF: 0.0785 Hom.: 844

Bravo AF: 0.0597

Asia WGS AF: 0.0690 AC: 241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.7
DANN	Benign	0.78
PhyloP100		0.21
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2280645; hg19: chr7-108524003; COSMIC: COSV66824141;