rs7637623

chr3-151611738-G-A

Variant summary

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

The NR_183765.1(LINC02066):n.106-24646G>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 0.581 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 NR_183765.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470

Genes affected

LINC02066 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02066	NR_183765.1	n.106-24646G>A		intron_variant, non_coding_transcript_variant
IGSF10	XM_011512709.3	c.-520+8168C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.630

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.703

Gnomad4 SAS AF: 0.625

Gnomad4 FIN AF: 0.583

Gnomad4 NFE AF: 0.554

Gnomad4 OTH AF: 0.566

Alfa AF: 0.567 Hom.: 12004

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7637623; hg19: chr3-151329526;