rs2439903

Positions:

• chr10-6789898-G-A

Variant summary

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

The ENST00000649110.1(LINC00707):​n.1019G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.093 in 152,104 control chromosomes in the GnomAD database, including 1,125 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 0.093 (1125 hom., cov: 31)
• Consequence: LINC00707 ENST00000649110.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181

Genes affected

LINC00707 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00707	NR_038291.1	n.473+8412G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00707	ENST00000649110.1	n.1019G>A		non_coding_transcript_exon_variant	3/3
LINC00707	ENST00000436383.2	n.501+8412G>A		intron_variant		2
LINC00707	ENST00000648093.1	n.522+8412G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0929 AC: 14121 AN: 151986 Hom.: 1119 Cov.: 31

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0700

Gnomad ASJ AF: 0.0807

Gnomad EAS AF: 0.0943

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0333

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0336

Gnomad OTH AF: 0.0785

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

GnomAD4 genome AF: 0.0930 AC: 14140 AN: 152104 Hom.: 1125 Cov.: 31 AF XY: 0.0936 AC XY: 6960 AN XY: 74356

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.0697

Gnomad4 ASJ AF: 0.0807

Gnomad4 EAS AF: 0.0940

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.0333

Gnomad4 NFE AF: 0.0336

Gnomad4 OTH AF: 0.0767

Alfa AF: 0.0458 Hom.: 536

Bravo AF: 0.101

Asia WGS AF: 0.100 AC: 348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.0
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2439903; hg19: chr10-6831860;