rs812845

Variant names:

• chr6-137693774-A-G
• rs812845
• ENST00000635999.1:n.433+19650A>G

Variant summary

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

The ENST00000635999.1(LINC03004):​n.433+19650A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 151,992 control chromosomes in the GnomAD database, including 22,089 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 0.52 (22089 hom., cov: 31)
• Consequence: LINC03004 ENST00000635999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 6 publications found

Genes affected

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

ENSG00000283265 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901411	XR_007059789.1	n.163+547A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03004	ENST00000635999.1	n.433+19650A>G		intron_variant	Intron 2 of 2	5
ENSG00000283265	ENST00000637996.1	n.160+547A>G		intron_variant	Intron 1 of 2	5
LINC03004	ENST00000646621.1	n.601+5085A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78842 AN: 151876 Hom.: 22053 Cov.: 31

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.519 AC: 78925 AN: 151992 Hom.: 22089 Cov.: 31 AF XY: 0.523 AC XY: 38847 AN XY: 74336

African (AFR) AF: 0.720 AC: 29833 AN: 41450

American (AMR) AF: 0.508 AC: 7769 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1316 AN: 3458

East Asian (EAS) AF: 0.804 AC: 4162 AN: 5176

South Asian (SAS) AF: 0.436 AC: 2100 AN: 4820

European-Finnish (FIN) AF: 0.474 AC: 4999 AN: 10552

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27224 AN: 67936

Other (OTH) AF: 0.520 AC: 1099 AN: 2112

Alfa AF: 0.469 Hom.: 2322

Bravo AF: 0.530

Asia WGS AF: 0.642 AC: 2231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
DANN	Benign	0.64
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs812845; hg19: chr6-138014911; COSMIC: COSV60285722;