6-137675748-A-T

Variant names:

• chr6-137675748-A-T
• rs665668
• ENST00000635999.1:n.433+1624A>T

Variant summary

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

The ENST00000635999.1(LINC03004):​n.433+1624A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 151,962 control chromosomes in the GnomAD database, including 21,614 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 0.53 (21614 hom., cov: 32)
• Consequence: LINC03004 ENST00000635999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121
• Publications: 5 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.585 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	ENST00000635999.1	n.433+1624A>T		intron_variant	Intron 2 of 2	5
LINC03004	ENST00000638039.2	n.438+1624A>T		intron_variant	Intron 2 of 4	5
LINC03004	ENST00000646621.1	n.414+1624A>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.533 AC: 80937 AN: 151844 Hom.: 21588 Cov.: 32

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.533 AC: 81004 AN: 151962 Hom.: 21614 Cov.: 32 AF XY: 0.528 AC XY: 39199 AN XY: 74278

African (AFR) AF: 0.591 AC: 24511 AN: 41446

American (AMR) AF: 0.513 AC: 7824 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.589 AC: 2042 AN: 3468

East Asian (EAS) AF: 0.457 AC: 2360 AN: 5168

South Asian (SAS) AF: 0.490 AC: 2360 AN: 4814

European-Finnish (FIN) AF: 0.448 AC: 4731 AN: 10566

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35328 AN: 67936

Other (OTH) AF: 0.512 AC: 1082 AN: 2112

Alfa AF: 0.521 Hom.: 2613

Bravo AF: 0.542

Asia WGS AF: 0.436 AC: 1513 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	1.3
DANN	Benign	0.52
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs665668; hg19: chr6-137996885;