rs11782819

Variant names:

• chr8-10477271-T-C
• rs11782819
• ENST00000517732.5:n.73T>C

Your query was ambiguous. Multiple possible variants found:

• chr8-10477271-T-C
• chr8-10477271-T-G

Variant summary

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

The ENST00000517732.5(LINC03022):​n.73T>C 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 0.536 in 152,118 control chromosomes in the GnomAD database, including 22,025 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 0.54 (22024 hom., cov: 32)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: LINC03022 ENST00000517732.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.715
• Publications: 16 publications found

Genes affected

LINC03022 (HGNC:56151): (long intergenic non-protein coding RNA 3022)

ENSG00000253678 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03022	NR_120604.1	n.216T>C		non_coding_transcript_exon_variant	Exon 2 of 5
LOC124901887	XR_007060821.1	n.746A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03022	ENST00000517732.5	n.73T>C		non_coding_transcript_exon_variant	Exon 1 of 4	4
LINC03022	ENST00000524047.5	n.216T>C		non_coding_transcript_exon_variant	Exon 2 of 5	4
ENSG00000253678	ENST00000649853.1	n.822A>G		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81452 AN: 151992 Hom.: 22009 Cov.: 32

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.580

GnomAD4 exome AF: 0.500 AC: 4 AN: 8 Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

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: 0.750 AC: 3 AN: 4

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: 0.536 AC: 81506 AN: 152110 Hom.: 22024 Cov.: 32 AF XY: 0.537 AC XY: 39929 AN XY: 74364

African (AFR) AF: 0.567 AC: 23536 AN: 41482

American (AMR) AF: 0.446 AC: 6817 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2262 AN: 3470

East Asian (EAS) AF: 0.604 AC: 3125 AN: 5176

South Asian (SAS) AF: 0.624 AC: 3008 AN: 4818

European-Finnish (FIN) AF: 0.549 AC: 5801 AN: 10562

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 35020 AN: 67994

Other (OTH) AF: 0.576 AC: 1215 AN: 2110

Alfa AF: 0.524 Hom.: 90866

Bravo AF: 0.527

Asia WGS AF: 0.573 AC: 1994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.18
DANN	Benign	0.38
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs11782819; hg19: chr8-10334781;