rs2709733

Variant names:

• chr7-20915751-G-A
• rs2709733
• ENST00000447262.2:n.151+32935G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000447262.2(LINC01162):​n.151+32935G>A variant causes a intron 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 ENST00000447262.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC01162	NR_126381.1	n.151+32935G>A		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01162	ENST00000447262.2	n.151+32935G>A		intron_variant	Intron 2 of 5	5
LINC01162	ENST00000661032.1	n.206+32935G>A		intron_variant	Intron 2 of 8
LINC01162	ENST00000742942.1	n.256+32935G>A		intron_variant	Intron 2 of 4

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

African (AFR) AF: 0.704 AC: 29191 AN: 41482

American (AMR) AF: 0.437 AC: 6665 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1799 AN: 3470

East Asian (EAS) AF: 0.566 AC: 2927 AN: 5170

South Asian (SAS) AF: 0.590 AC: 2840 AN: 4812

European-Finnish (FIN) AF: 0.473 AC: 4993 AN: 10556

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.462 AC: 31370 AN: 67948

Other (OTH) AF: 0.556 AC: 1173 AN: 2110

Alfa AF: 0.480 Hom.: 28979

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2709733; hg19: chr7-20955370;