rs2207337

chr6-29232468-T-Achr6-29232468-T-C

Variant summary

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

The XR_001744077.2(LOC105375006):n.83A>T 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 0.556 in 151,934 control chromosomes in the GnomAD database, including 25,104 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 0.56 (25104 hom., cov: 31)
• Consequence: LOC105375006 XR_001744077.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290

Genes affected

LOC105375006 (HGNC:):

LINC03003 (HGNC:56126): (long intergenic non-protein coding RNA 3003)

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 (NFE) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375006	XR_001744077.2	n.83A>T		non_coding_transcript_exon_variant	2/3
LINC03003	NR_134630.1	n.79+8417T>A		intron_variant, non_coding_transcript_variant
LINC03003	NR_134629.1	n.79+8417T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03003	ENST00000606648.1	n.52+8417T>A		intron_variant, non_coding_transcript_variant		3
LINC03003	ENST00000441381.1	n.79+8417T>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84430 AN: 151816 Hom.: 25107 Cov.: 31

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.556 AC: 84446 AN: 151934 Hom.: 25104 Cov.: 31 AF XY: 0.564 AC XY: 41894 AN XY: 74262

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.626

Gnomad4 EAS AF: 0.473

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.772

Gnomad4 NFE AF: 0.650

Gnomad4 OTH AF: 0.547

Alfa AF: 0.605 Hom.: 3603

Bravo AF: 0.522

Asia WGS AF: 0.607 AC: 2111 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	9.8
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2207337; hg19: chr6-29200245;