rs1419410

Variant names:

• chr7-127480443-C-G
• rs1419410
• ENST00000448311.1:n.264+1206C>G

Variant summary

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

The ENST00000448311.1(LINC03012):​n.264+1206C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,108 control chromosomes in the GnomAD database, including 7,191 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 0.27 (7191 hom., cov: 32)
• Consequence: LINC03012 ENST00000448311.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.863
• Publications: 5 publications found

Genes affected

LINC03012 (HGNC:56139): (long intergenic non-protein coding RNA 3012)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000448311.1. 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
	LINC03012	NR_110024.1		n.264+1206C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03012	ENST00000448311.1	TSL:2	n.264+1206C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40815 AN: 151990 Hom.: 7186 Cov.: 32

Gnomad AFR AF: 0.0658

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.268 AC: 40818 AN: 152108 Hom.: 7191 Cov.: 32 AF XY: 0.277 AC XY: 20599 AN XY: 74340

African (AFR) AF: 0.0656 AC: 2725 AN: 41530

American (AMR) AF: 0.298 AC: 4562 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 676 AN: 3470

East Asian (EAS) AF: 0.671 AC: 3473 AN: 5176

South Asian (SAS) AF: 0.317 AC: 1523 AN: 4806

European-Finnish (FIN) AF: 0.426 AC: 4482 AN: 10532

Middle Eastern (MID) AF: 0.130 AC: 38 AN: 292

European-Non Finnish (NFE) AF: 0.330 AC: 22433 AN: 67984

Other (OTH) AF: 0.262 AC: 553 AN: 2110

Alfa AF: 0.299 Hom.: 1087

Bravo AF: 0.252

Asia WGS AF: 0.449 AC: 1556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.74
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs1419410; hg19: chr7-127120497;