6-137678149-C-T

Position:

• chr6-137678149-C-T

Variant summary

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

The variant allele was found at a frequency of 0.621 in 151,814 control chromosomes in the GnomAD database, including 29,564 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 0.62 (29564 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.137678149C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC03004	ENST00000635999.1	n.433+4025C>T		intron_variant		5
LINC03004	ENST00000638039.1	n.438+4025C>T		intron_variant		5
LINC03004	ENST00000646621.1	n.414+4025C>T		intron_variant
LINC03004	ENST00000666119.1	n.392+4025C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94294 AN: 151696 Hom.: 29541 Cov.: 30

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.621 AC: 94350 AN: 151814 Hom.: 29564 Cov.: 30 AF XY: 0.621 AC XY: 46014 AN XY: 74156

Gnomad4 AFR AF: 0.695

Gnomad4 AMR AF: 0.551

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.734

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.634

Gnomad4 NFE AF: 0.595

Gnomad4 OTH AF: 0.617

Alfa AF: 0.526 Hom.: 2533

Bravo AF: 0.617

Asia WGS AF: 0.634 AC: 2202 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.4
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9376293; hg19: chr6-137999286; COSMIC: COSV71077270;