rs11254686

chr10-6796980-C-T

Variant summary

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

The NR_038291.1(LINC00707):n.473+15494C>T 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 0.0926 in 152,170 control chromosomes in the GnomAD database, including 821 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 (821 hom., cov: 31)
• Consequence: LINC00707 NR_038291.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13

Genes affected

LINC00707 (HGNC:44691): (long intergenic non-protein coding RNA 707)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00707	NR_038291.1	n.473+15494C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00707	ENST00000436383.2	n.501+15494C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0925 AC: 14064 AN: 152052 Hom.: 817 Cov.: 31

Gnomad AFR AF: 0.0466

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.0758

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.0745

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.0926 AC: 14084 AN: 152170 Hom.: 821 Cov.: 31 AF XY: 0.0940 AC XY: 6990 AN XY: 74380

Gnomad4 AFR AF: 0.0469

Gnomad4 AMR AF: 0.0756

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.217

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.0745

Gnomad4 NFE AF: 0.100

Gnomad4 OTH AF: 0.117

Alfa AF: 0.0888 Hom.: 115

Bravo AF: 0.0900

Asia WGS AF: 0.184 AC: 639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	3.4
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11254686; hg19: chr10-6838942;