1-72285502-T-C

Variant names:

• chr1-72285502-T-C
• rs3101336
• ENST00000715640.2:n.236+2097T>C

Variant summary

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

The ENST00000715640.2(LINC02796):​n.236+2097T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 152,064 control chromosomes in the GnomAD database, including 30,327 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 0.62 (30327 hom., cov: 33)
• Consequence: LINC02796 ENST00000715640.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.699
• Publications: 140 publications found

Genes affected

LINC02796 (HGNC:27918): (long intergenic non-protein coding RNA 2796)

LOC105378797 (HGNC:):

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 = 0.901 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378797	XR_001737670.2	n.472+2097T>C		intron_variant	Intron 1 of 7
LOC105378797	XR_001737671.3	n.472+2097T>C		intron_variant	Intron 1 of 5
LOC105378797	XR_947505.3	n.472+2097T>C		intron_variant	Intron 1 of 6
LOC105378797	XR_947506.3	n.472+2097T>C		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02796	ENST00000715640.2	n.236+2097T>C		intron_variant	Intron 1 of 6
LINC02796	ENST00000715641.1	n.227+2097T>C		intron_variant	Intron 1 of 2
LINC02796	ENST00000715642.1	n.153+2097T>C		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.625 AC: 94968 AN: 151946 Hom.: 30313 Cov.: 33

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.639

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.625 AC: 95014 AN: 152064 Hom.: 30327 Cov.: 33 AF XY: 0.631 AC XY: 46931 AN XY: 74334

African (AFR) AF: 0.540 AC: 22376 AN: 41444

American (AMR) AF: 0.708 AC: 10828 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.735 AC: 2552 AN: 3470

East Asian (EAS) AF: 0.923 AC: 4783 AN: 5182

South Asian (SAS) AF: 0.668 AC: 3223 AN: 4824

European-Finnish (FIN) AF: 0.649 AC: 6848 AN: 10556

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.623 AC: 42328 AN: 67984

Other (OTH) AF: 0.643 AC: 1357 AN: 2112

Alfa AF: 0.628 Hom.: 91130

Bravo AF: 0.628

Asia WGS AF: 0.752 AC: 2613 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	11
DANN	Benign	0.80
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs3101336; hg19: chr1-72751185;