7-84570245-A-G

Position:

• chr7-84570245-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_110080.1(LINC03017):​n.240-734A>G variant causes a intron, non coding transcript 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 NR_110080.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC03017	NR_110080.1	n.240-734A>G		intron_variant, non_coding_transcript_variant
LINC03017	NR_110079.1	n.240-734A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC03017	ENST00000450977.2	n.240-734A>G		intron_variant, non_coding_transcript_variant		1
LINC03017	ENST00000446000.1	n.49-734A>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.611

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.819

Gnomad4 SAS AF: 0.565

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.535

Alfa AF: 0.448 Hom.: 1989

Bravo AF: 0.529

Asia WGS AF: 0.700 AC: 2429 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs722453; hg19: chr7-84199561;