rs6917441

Positions:

• chr6-137697302-A-G

Variant summary

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

The ENST00000635999.1(LINC03004):​n.433+23178A>G 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 0.301 in 152,132 control chromosomes in the GnomAD database, including 7,147 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 0.30 (7147 hom., cov: 33)
• Consequence: LINC03004 ENST00000635999.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320

Genes affected

LINC03004 (HGNC:56128): (long intergenic non-protein coding RNA 3004)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901411	XR_007059789.1	n.164-1375A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC03004	ENST00000635999.1	n.433+23178A>G		intron_variant, non_coding_transcript_variant		5
	ENST00000637996.1	n.161-1375A>G		intron_variant, non_coding_transcript_variant		5
LINC03004	ENST00000646621.1	n.601+8613A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45799 AN: 152014 Hom.: 7149 Cov.: 33

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.301 AC: 45803 AN: 152132 Hom.: 7147 Cov.: 33 AF XY: 0.308 AC XY: 22923 AN XY: 74384

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.536

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.310

Alfa AF: 0.260 Hom.: 10853

Bravo AF: 0.300

Asia WGS AF: 0.410 AC: 1426 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6917441; hg19: chr6-138018439;