ENST00000746620.1:n.105+3940A>G

Variant names:

• chr6-137651931-A-G
• rs2327832
• ENST00000746620.1:n.105+3940A>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+3940A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,154 control chromosomes in the GnomAD database, including 2,121 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 (2121 hom., cov: 31)
• Consequence: LINC03004 ENST00000746620.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.477
• Publications: 98 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 (NFE) allele frequency at 95% confidence interval = 0.206 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+3940A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24135 AN: 152036 Hom.: 2120 Cov.: 31

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.159 AC: 24140 AN: 152154 Hom.: 2121 Cov.: 31 AF XY: 0.154 AC XY: 11465 AN XY: 74372

African (AFR) AF: 0.110 AC: 4562 AN: 41518

American (AMR) AF: 0.124 AC: 1895 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 520 AN: 3472

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5180

South Asian (SAS) AF: 0.120 AC: 579 AN: 4812

European-Finnish (FIN) AF: 0.177 AC: 1873 AN: 10584

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14183 AN: 67998

Other (OTH) AF: 0.159 AC: 334 AN: 2106

Alfa AF: 0.189 Hom.: 11973

Bravo AF: 0.153

Asia WGS AF: 0.0610 AC: 213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.6
DANN	Benign	0.74
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs2327832; hg19: chr6-137973068;