10-31239873-T-G

Position:

• chr10-31239873-T-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000605929.1(LINC02664):​n.318-20109T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.856 in 152,104 control chromosomes in the GnomAD database, including 58,263 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 0.86 (58263 hom., cov: 32)
• Consequence: LINC02664 ENST00000605929.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125

Genes affected

LINC02664 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.984 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02664	NR_134478.1	n.318-20109T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02664	ENST00000605929.1	n.318-20109T>G		intron_variant		2
ZEB1-AS1	ENST00000605946.1	n.178-33391A>C		intron_variant		5
LINC02664	ENST00000662544.1	n.390-8654T>G		intron_variant
LINC02664	ENST00000669722.1	n.609-20109T>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.856 AC: 130066 AN: 151986 Hom.: 58242 Cov.: 32

Gnomad AFR AF: 0.563

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.926

Gnomad ASJ AF: 0.894

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.914

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.990

Gnomad OTH AF: 0.871

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

GnomAD4 genome AF: 0.856 AC: 130129 AN: 152104 Hom.: 58263 Cov.: 32 AF XY: 0.858 AC XY: 63777 AN XY: 74342

Gnomad4 AFR AF: 0.563

Gnomad4 AMR AF: 0.926

Gnomad4 ASJ AF: 0.894

Gnomad4 EAS AF: 0.820

Gnomad4 SAS AF: 0.915

Gnomad4 FIN AF: 0.997

Gnomad4 NFE AF: 0.990

Gnomad4 OTH AF: 0.874

Alfa AF: 0.957 Hom.: 23685

Bravo AF: 0.835

Asia WGS AF: 0.864 AC: 2996 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	14
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3123688; hg19: chr10-31528802;