rs2709733

Positions:

• chr7-20915751-G-A
• chr7-20915751-G-C

Variant summary

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

The NR_126381.1(LINC01162):​n.151+32935G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 152,018 control chromosomes in the GnomAD database, including 22,809 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 0.54 (22809 hom., cov: 32)
• Consequence: LINC01162 NR_126381.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

Genes affected

LINC01162 (HGNC:49528): (long intergenic non-protein coding RNA 1162)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01162	NR_126381.1	n.151+32935G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01162	ENST00000661032.1	n.206+32935G>A		intron_variant, non_coding_transcript_variant
LINC01162	ENST00000447262.2	n.151+32935G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81463 AN: 151902 Hom.: 22796 Cov.: 32

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.567

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.536 AC: 81511 AN: 152018 Hom.: 22809 Cov.: 32 AF XY: 0.535 AC XY: 39716 AN XY: 74296

Gnomad4 AFR AF: 0.704

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.566

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.556

Alfa AF: 0.471 Hom.: 19156

Bravo AF: 0.539

Asia WGS AF: 0.619 AC: 2146 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.031
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2709733; hg19: chr7-20955370;