rs665668

Positions:

• chr6-137675748-A-T

Variant summary

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

The ENST00000635999.1(LINC03004):​n.433+1624A>T 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 0.533 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121

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 (AFR) allele frequency at 95% confidence interval = 0.585 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+1624A>T		intron_variant, non_coding_transcript_variant		5
LINC03004	ENST00000638039.1	n.438+1624A>T		intron_variant, non_coding_transcript_variant		5
LINC03004	ENST00000646621.1	n.414+1624A>T		intron_variant, non_coding_transcript_variant
LINC03004	ENST00000666119.1	n.392+1624A>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.591

Gnomad4 AMR AF: 0.513

Gnomad4 ASJ AF: 0.589

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.490

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.512

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs665668; hg19: chr6-137996885;