rs17264332

Positions:

• chr6-137684378-A-G
• chr6-137684378-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+10254A>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 0.158 in 152,120 control chromosomes in the GnomAD database, including 2,102 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 0.16 (2102 hom., cov: 33)
• Consequence: LINC03004 ENST00000635999.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.252

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 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+10254A>G		intron_variant, non_coding_transcript_variant		5
LINC03004	ENST00000638039.1	n.439-2716A>G		intron_variant, non_coding_transcript_variant		5
LINC03004	ENST00000646621.1	n.415-2716A>G		intron_variant, non_coding_transcript_variant
LINC03004	ENST00000666119.1	n.393-2716A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24021 AN: 152002 Hom.: 2100 Cov.: 33

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.158 AC: 24030 AN: 152120 Hom.: 2102 Cov.: 33 AF XY: 0.154 AC XY: 11419 AN XY: 74370

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.159

Alfa AF: 0.113 Hom.: 253

Bravo AF: 0.152

Asia WGS AF: 0.0500 AC: 175 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.9
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17264332; hg19: chr6-138005515;