10-31207045-G-A

Position:

• chr10-31207045-G-A

Variant summary

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

The ENST00000605929.1(LINC02664):​n.317+18846G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.803 in 152,202 control chromosomes in the GnomAD database, including 54,454 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 0.80 (54454 hom., cov: 33)
• Consequence: LINC02664 ENST00000605929.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363

Genes affected

LINC02664 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.983 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02664	NR_134478.1	n.317+18846G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02664	ENST00000605929.1	n.317+18846G>A		intron_variant		2
ZEB1-AS1	ENST00000605946.1	n.178-563C>T		intron_variant		5
LINC02664	ENST00000662544.1	n.389+181G>A		intron_variant
LINC02664	ENST00000669722.1	n.608+181G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.803 AC: 122173 AN: 152084 Hom.: 54451 Cov.: 33

Gnomad AFR AF: 0.382

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.906

Gnomad ASJ AF: 0.891

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.913

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.990

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.803 AC: 122187 AN: 152202 Hom.: 54454 Cov.: 33 AF XY: 0.807 AC XY: 60027 AN XY: 74414

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.906

Gnomad4 ASJ AF: 0.891

Gnomad4 EAS AF: 0.806

Gnomad4 SAS AF: 0.914

Gnomad4 FIN AF: 0.997

Gnomad4 NFE AF: 0.990

Gnomad4 OTH AF: 0.840

Alfa AF: 0.785 Hom.: 2350

Bravo AF: 0.776

Asia WGS AF: 0.848 AC: 2951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.34
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1250307; hg19: chr10-31495974;