chr6-137692414-A-G

Position:

• chr6-137692414-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+18290A>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 0.658 in 152,128 control chromosomes in the GnomAD database, including 33,468 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 0.66 (33468 hom., cov: 33)
• Consequence: LINC03004 ENST00000635999.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC03004	ENST00000635999.1	n.433+18290A>G		intron_variant, non_coding_transcript_variant		5
LINC03004	ENST00000646621.1	n.601+3725A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.658 AC: 100017 AN: 152010 Hom.: 33423 Cov.: 33

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.658 AC: 100111 AN: 152128 Hom.: 33468 Cov.: 33 AF XY: 0.658 AC XY: 48939 AN XY: 74356

Gnomad4 AFR AF: 0.767

Gnomad4 AMR AF: 0.624

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.806

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.650

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.657

Alfa AF: 0.632 Hom.: 5258

Bravo AF: 0.659

Asia WGS AF: 0.689 AC: 2395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.62
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs694069; hg19: chr6-138013551; COSMIC: COSV60285697;