rs6953213

Variant names:

• chr7-7273854-G-A
• rs6953213
• ENST00000430266.2:n.277-3731G>A

Variant summary

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

The ENST00000436578.2(LINC03016):​n.564-3731G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0577 in 152,138 control chromosomes in the GnomAD database, including 333 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 0.058 (333 hom., cov: 32)
• Consequence: LINC03016 ENST00000436578.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.499
• Publications: 2 publications found

Genes affected

LINC03016 (HGNC:56145): (long intergenic non-protein coding RNA 3016)

LOC107986764 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000436578.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03016	NR_108073.1		n.277-3731G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03016	ENST00000430266.2	TSL:5	n.277-3731G>A		intron	N/A
	LINC03016	ENST00000436578.2	TSL:3	n.564-3731G>A		intron	N/A
	LINC03016	ENST00000447039.1	TSL:3	n.437+2010G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0577 AC: 8777 AN: 152022 Hom.: 334 Cov.: 32

Gnomad AFR AF: 0.0739

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.0604

Gnomad ASJ AF: 0.0567

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.0242

Gnomad FIN AF: 0.0857

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0354

Gnomad OTH AF: 0.0430

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

GnomAD4 genome AF: 0.0577 AC: 8782 AN: 152138 Hom.: 333 Cov.: 32 AF XY: 0.0606 AC XY: 4506 AN XY: 74372

African (AFR) AF: 0.0739 AC: 3067 AN: 41506

American (AMR) AF: 0.0606 AC: 926 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0567 AC: 197 AN: 3472

East Asian (EAS) AF: 0.180 AC: 928 AN: 5146

South Asian (SAS) AF: 0.0241 AC: 116 AN: 4822

European-Finnish (FIN) AF: 0.0857 AC: 907 AN: 10582

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0354 AC: 2406 AN: 67998

Other (OTH) AF: 0.0421 AC: 89 AN: 2116

Alfa AF: 0.0526 Hom.: 44

Bravo AF: 0.0577

Asia WGS AF: 0.100 AC: 351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.3
DANN	Benign	0.78
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs6953213; hg19: chr7-7313485;