7-84570245-A-G

Variant names:

• chr7-84570245-A-G
• rs722453
• ENST00000450977.2:n.240-734A>G

Variant summary

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

The ENST00000450977.2(LINC03017):​n.240-734A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 151,100 control chromosomes in the GnomAD database, including 20,300 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 0.50 (20300 hom., cov: 31)
• Consequence: LINC03017 ENST00000450977.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193
• Publications: 1 publications found

Genes affected

LINC03017 (HGNC:56146): (long intergenic non-protein coding RNA 3017)

ENSG00000301054 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000450977.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03017	NR_110079.1		n.240-734A>G		intron	N/A
	LINC03017	NR_110080.1		n.240-734A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03017	ENST00000450977.2	TSL:1	n.240-734A>G		intron	N/A
	LINC03017	ENST00000446000.2	TSL:3	n.190-734A>G		intron	N/A
	ENSG00000301054	ENST00000775795.1		n.139-4156T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.503 AC: 75898 AN: 150982 Hom.: 20261 Cov.: 31

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.503 AC: 75995 AN: 151100 Hom.: 20300 Cov.: 31 AF XY: 0.502 AC XY: 37047 AN XY: 73800

African (AFR) AF: 0.611 AC: 25230 AN: 41288

American (AMR) AF: 0.585 AC: 8836 AN: 15106

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1788 AN: 3450

East Asian (EAS) AF: 0.819 AC: 4138 AN: 5052

South Asian (SAS) AF: 0.565 AC: 2724 AN: 4818

European-Finnish (FIN) AF: 0.301 AC: 3179 AN: 10546

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28396 AN: 67534

Other (OTH) AF: 0.535 AC: 1124 AN: 2100

Alfa AF: 0.454 Hom.: 2130

Bravo AF: 0.529

Asia WGS AF: 0.700 AC: 2429 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.38
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs722453; hg19: chr7-84199561;