rs6943606

chr7-25786929-C-Achr7-25786929-C-G

Variant summary

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

The NR_157808.1(LINC03007):n.367+2824G>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 0.0632 in 152,272 control chromosomes in the GnomAD database, including 575 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 0.063 (575 hom., cov: 33)
• Consequence: LINC03007 NR_157808.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.325

Genes affected

LINC03007 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC03007	NR_157808.1	n.367+2824G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0631 AC: 9608 AN: 152154 Hom.: 572 Cov.: 33

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0891

Gnomad ASJ AF: 0.0132

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.0455

Gnomad FIN AF: 0.00613

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0165

Gnomad OTH AF: 0.0569

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

GnomAD4 genome AF: 0.0632 AC: 9623 AN: 152272 Hom.: 575 Cov.: 33 AF XY: 0.0618 AC XY: 4605 AN XY: 74456

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.0894

Gnomad4 ASJ AF: 0.0132

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.0456

Gnomad4 FIN AF: 0.00613

Gnomad4 NFE AF: 0.0165

Gnomad4 OTH AF: 0.0587

Alfa AF: 0.0361 Hom.: 87

Bravo AF: 0.0770

Asia WGS AF: 0.115 AC: 400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	6.0
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6943606; hg19: chr7-25826549;