6-137649927-T-G

Variant names:

• chr6-137649927-T-G
• rs928720
• ENST00000746620.1:n.105+1936T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000746620.1(LINC03004):​n.105+1936T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 151,776 control chromosomes in the GnomAD database, including 14,391 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 0.43 (14391 hom., cov: 30)
• Consequence: LINC03004 ENST00000746620.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.434
• Publications: 7 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03004	ENST00000746620.1	n.105+1936T>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65739 AN: 151658 Hom.: 14386 Cov.: 30

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.433 AC: 65760 AN: 151776 Hom.: 14391 Cov.: 30 AF XY: 0.437 AC XY: 32423 AN XY: 74162

African (AFR) AF: 0.364 AC: 15044 AN: 41374

American (AMR) AF: 0.417 AC: 6349 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1376 AN: 3470

East Asian (EAS) AF: 0.528 AC: 2727 AN: 5160

South Asian (SAS) AF: 0.442 AC: 2128 AN: 4814

European-Finnish (FIN) AF: 0.529 AC: 5553 AN: 10506

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31207 AN: 67912

Other (OTH) AF: 0.449 AC: 945 AN: 2104

Alfa AF: 0.393 Hom.: 2870

Bravo AF: 0.422

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.59
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs928720; hg19: chr6-137971064;