rs1679456

Positions:

• chr10-4407554-C-A

Variant summary

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

The ENST00000434902.1(LINC00703):​n.73-901C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,110 control chromosomes in the GnomAD database, including 1,342 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 0.12 (1342 hom., cov: 32)
• Consequence: LINC00703 ENST00000434902.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.682

Genes affected

LINC00703 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00703	NR_108054.1	n.336-901C>A		intron_variant
LINC00703	NR_108055.1	n.233-901C>A		intron_variant
LINC00703	NR_108056.1	n.106-901C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00703	ENST00000434902.1	n.73-901C>A		intron_variant		2
LINC00703	ENST00000454152.1	n.233-901C>A		intron_variant		2
LINC00703	ENST00000655424.1	n.149-901C>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18814 AN: 151992 Hom.: 1340 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0919

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.124 AC: 18847 AN: 152110 Hom.: 1342 Cov.: 32 AF XY: 0.127 AC XY: 9418 AN XY: 74346

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.0919

Gnomad4 OTH AF: 0.127

Alfa AF: 0.106 Hom.: 444

Bravo AF: 0.124

Asia WGS AF: 0.272 AC: 946 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1679456; hg19: chr10-4449746;