chr7-7262662-G-A

Variant names:

• chr7-7262662-G-A
• rs1299548
• ENST00000430266.2:n.70+3066G>A

Variant summary

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

The ENST00000430266.2(LINC03016):​n.70+3066G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 152,066 control chromosomes in the GnomAD database, including 21,981 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 0.52 (21981 hom., cov: 32)
• Consequence: LINC03016 ENST00000430266.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220
• Publications: 15 publications found

Genes affected

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

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 (AFR) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03016	NR_108073.1	n.70+3066G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03016	ENST00000430266.2	n.70+3066G>A		intron_variant	Intron 2 of 3	5
LINC03016	ENST00000657192.2	n.258-4575G>A		intron_variant	Intron 1 of 2
LINC03016	ENST00000659742.1	n.70+3066G>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79535 AN: 151948 Hom.: 21945 Cov.: 32

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.524 AC: 79617 AN: 152066 Hom.: 21981 Cov.: 32 AF XY: 0.515 AC XY: 38302 AN XY: 74328

African (AFR) AF: 0.697 AC: 28877 AN: 41460

American (AMR) AF: 0.434 AC: 6637 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 2203 AN: 3470

East Asian (EAS) AF: 0.240 AC: 1240 AN: 5174

South Asian (SAS) AF: 0.380 AC: 1835 AN: 4826

European-Finnish (FIN) AF: 0.446 AC: 4714 AN: 10562

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32408 AN: 67978

Other (OTH) AF: 0.530 AC: 1119 AN: 2110

Alfa AF: 0.492 Hom.: 84895

Bravo AF: 0.532

Asia WGS AF: 0.345 AC: 1200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.81
DANN	Benign	0.14
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs1299548; hg19: chr7-7302293;