7-7273854-G-A

Position:

• chr7-7273854-G-A

Variant summary

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

The ENST00000436578.1(LINC03016):​n.536-3731G>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 ENST00000436578.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.499

Genes affected

LINC03016 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC03016	NR_108073.1	n.277-3731G>A		intron_variant
LOC107986764	XR_002956539.2	n.441+2010G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC03016	ENST00000430266.2	n.277-3731G>A		intron_variant		5
LINC03016	ENST00000436578.1	n.536-3731G>A		intron_variant		3
LINC03016	ENST00000447039.1	n.437+2010G>A		intron_variant		3

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

Gnomad4 AFR AF: 0.0739

Gnomad4 AMR AF: 0.0606

Gnomad4 ASJ AF: 0.0567

Gnomad4 EAS AF: 0.180

Gnomad4 SAS AF: 0.0241

Gnomad4 FIN AF: 0.0857

Gnomad4 NFE AF: 0.0354

Gnomad4 OTH AF: 0.0421

Alfa AF: 0.0522 Hom.: 42

Bravo AF: 0.0577

Asia WGS AF: 0.100 AC: 351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6953213; hg19: chr7-7313485;