rs11209979

Variant names:

• chr1-72563930-T-A
• rs11209979
• ENST00000715640.2:n.710+5944T>A

Variant summary

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

The ENST00000715640.2(LINC02796):​n.710+5944T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 151,938 control chromosomes in the GnomAD database, including 3,628 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 0.21 (3628 hom., cov: 32)
• Consequence: LINC02796 ENST00000715640.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.241
• Publications: 3 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378797	XR_001737670.2	n.964+5944T>A		intron_variant	Intron 5 of 7
LOC105378797	XR_001737671.3	n.646+5944T>A		intron_variant	Intron 3 of 5
LOC105378797	XR_947505.3	n.834+5944T>A		intron_variant	Intron 4 of 6
LOC105378797	XR_947506.3	n.786+5944T>A		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02796	ENST00000715640.2	n.710+5944T>A		intron_variant	Intron 5 of 6
LINC02796	ENST00000715642.1	n.515+5944T>A		intron_variant	Intron 4 of 6
LINC02796	ENST00000715643.1	n.530+5944T>A		intron_variant	Intron 5 of 7

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32002 AN: 151820 Hom.: 3619 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.0281

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.211 AC: 32040 AN: 151938 Hom.: 3628 Cov.: 32 AF XY: 0.202 AC XY: 15039 AN XY: 74288

African (AFR) AF: 0.204 AC: 8441 AN: 41438

American (AMR) AF: 0.214 AC: 3270 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 795 AN: 3466

East Asian (EAS) AF: 0.0279 AC: 145 AN: 5190

South Asian (SAS) AF: 0.124 AC: 597 AN: 4822

European-Finnish (FIN) AF: 0.127 AC: 1341 AN: 10582

Middle Eastern (MID) AF: 0.205 AC: 60 AN: 292

European-Non Finnish (NFE) AF: 0.247 AC: 16742 AN: 67874

Other (OTH) AF: 0.216 AC: 455 AN: 2108

Alfa AF: 0.236 Hom.: 537

Bravo AF: 0.216

Asia WGS AF: 0.0890 AC: 307 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.3
DANN	Benign	0.38
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs11209979; hg19: chr1-73029613;