rs73161338

Variant names:

• chr7-155392165-G-A
• rs73161338
• ENST00000401499.2:n.649-2881G>A

Variant summary

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

The ENST00000401499.2(LINC03010):​n.649-2881G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0898 in 152,238 control chromosomes in the GnomAD database, including 657 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 0.090 (657 hom., cov: 33)
• Consequence: LINC03010 ENST00000401499.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.450
• Publications: 1 publications found

Genes affected

LINC03010 (HGNC:56135): (long intergenic non-protein coding RNA 3010)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03010	NR_147174.1	n.241-2881G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03010	ENST00000401499.2	n.649-2881G>A		intron_variant	Intron 1 of 1	1
LINC03010	ENST00000765361.1	n.279-2881G>A		intron_variant	Intron 1 of 2
LINC03010	ENST00000765362.1	n.273-2881G>A		intron_variant	Intron 1 of 2
LINC03010	ENST00000765363.1	n.441+677G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0897 AC: 13642 AN: 152120 Hom.: 656 Cov.: 33

Gnomad AFR AF: 0.0750

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.0626

Gnomad ASJ AF: 0.0833

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0596

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0870

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

GnomAD4 genome AF: 0.0898 AC: 13665 AN: 152238 Hom.: 657 Cov.: 33 AF XY: 0.0870 AC XY: 6477 AN XY: 74448

African (AFR) AF: 0.0753 AC: 3126 AN: 41532

American (AMR) AF: 0.0625 AC: 956 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0833 AC: 289 AN: 3470

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5184

South Asian (SAS) AF: 0.0605 AC: 292 AN: 4826

European-Finnish (FIN) AF: 0.103 AC: 1098 AN: 10612

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7497 AN: 67998

Other (OTH) AF: 0.0861 AC: 182 AN: 2114

Alfa AF: 0.106 Hom.: 178

Bravo AF: 0.0853

Asia WGS AF: 0.0330 AC: 116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.0
DANN	Benign	0.84
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs73161338; hg19: chr7-155184860;