rs7637623

Variant names:

• chr3-151611738-G-A
• rs7637623
• ENST00000492731.2:n.132-15456G>A

Variant summary

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

The ENST00000492731.2(LINC02066):​n.132-15456G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 152,002 control chromosomes in the GnomAD database, including 25,834 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 0.58 (25834 hom., cov: 32)
• Consequence: LINC02066 ENST00000492731.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470
• Publications: 1 publications found

Genes affected

LINC02066 (HGNC:52911): (long intergenic non-protein coding RNA 2066)

AADACL2-AS1 (HGNC:50301): (AADACL2 antisense RNA 1)

IGSF10 (HGNC:26384): (immunoglobulin superfamily member 10) Predicted to be involved in regulation of neuron migration. Predicted to act upstream of or within ossification. Located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02066	NR_183765.1	n.106-24646G>A		intron_variant	Intron 1 of 4
IGSF10	XM_011512709.3	c.-520+8168C>T		intron_variant	Intron 1 of 10		XP_011511011.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02066	ENST00000492731.2	n.132-15456G>A		intron_variant	Intron 1 of 5	4
AADACL2-AS1	ENST00000754423.1	n.452-10787C>T		intron_variant	Intron 3 of 5
LINC02066	ENST00000754497.1	n.155-24646G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88170 AN: 151886 Hom.: 25799 Cov.: 32

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.702

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.581 AC: 88256 AN: 152002 Hom.: 25834 Cov.: 32 AF XY: 0.583 AC XY: 43318 AN XY: 74296

African (AFR) AF: 0.630 AC: 26110 AN: 41460

American (AMR) AF: 0.528 AC: 8066 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1807 AN: 3464

East Asian (EAS) AF: 0.703 AC: 3640 AN: 5180

South Asian (SAS) AF: 0.625 AC: 3017 AN: 4824

European-Finnish (FIN) AF: 0.583 AC: 6159 AN: 10558

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.554 AC: 37633 AN: 67934

Other (OTH) AF: 0.566 AC: 1195 AN: 2112

Alfa AF: 0.565 Hom.: 13186

Bravo AF: 0.577

Asia WGS AF: 0.658 AC: 2286 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.7
DANN	Benign	0.61
PhyloP100		0.047

Splicing

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

Other links and lift over

dbSNP: rs7637623; hg19: chr3-151329526;