7-20954872-A-G

Position:

• chr7-20954872-A-G

Variant summary

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

The NR_126381.1(LINC01162):​n.152-65996A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.812 in 152,160 control chromosomes in the GnomAD database, including 50,329 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 0.81 (50329 hom., cov: 31)
• Consequence: LINC01162 NR_126381.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350

Genes affected

LINC01162 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01162	NR_126381.1	n.152-65996A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01162	ENST00000447262.2	n.152-65996A>G		intron_variant		5
LINC01162	ENST00000661032.1	n.207-5808A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123402 AN: 152042 Hom.: 50275 Cov.: 31

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.785

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.802

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.812 AC: 123516 AN: 152160 Hom.: 50329 Cov.: 31 AF XY: 0.811 AC XY: 60331 AN XY: 74388

Gnomad4 AFR AF: 0.875

Gnomad4 AMR AF: 0.857

Gnomad4 ASJ AF: 0.785

Gnomad4 EAS AF: 0.745

Gnomad4 SAS AF: 0.801

Gnomad4 FIN AF: 0.765

Gnomad4 NFE AF: 0.776

Gnomad4 OTH AF: 0.833

Alfa AF: 0.783 Hom.: 85741

Bravo AF: 0.823

Asia WGS AF: 0.796 AC: 2765 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	1.6
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12155172; hg19: chr7-20994491;