12-8452666-T-C

Variant names:

• chr12-8452666-T-C
• rs11045418
• ENST00000693495.2:n.127+345A>G

Variant summary

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

The ENST00000693495.2(LINC00937):​n.127+345A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,108 control chromosomes in the GnomAD database, including 6,983 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 0.30 (6983 hom., cov: 32)
• Consequence: LINC00937 ENST00000693495.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.724
• Publications: 4 publications found

Genes affected

LINC00937 (HGNC:48629): (long intergenic non-protein coding RNA 937)

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 (EAS) allele frequency at 95% confidence interval = 0.47 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
LINC00937	ENST00000693495.2	n.127+345A>G		intron_variant	Intron 1 of 3
LINC00937	ENST00000734929.1	n.151+345A>G		intron_variant	Intron 1 of 7
LINC00937	ENST00000734930.1	n.151+345A>G		intron_variant	Intron 1 of 2
LINC00937	ENST00000735009.1	n.83+345A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45110 AN: 151990 Hom.: 6974 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.297 AC: 45151 AN: 152108 Hom.: 6983 Cov.: 32 AF XY: 0.300 AC XY: 22292 AN XY: 74364

African (AFR) AF: 0.248 AC: 10273 AN: 41486

American (AMR) AF: 0.284 AC: 4346 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 773 AN: 3472

East Asian (EAS) AF: 0.486 AC: 2514 AN: 5178

South Asian (SAS) AF: 0.413 AC: 1988 AN: 4816

European-Finnish (FIN) AF: 0.310 AC: 3278 AN: 10580

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21041 AN: 67972

Other (OTH) AF: 0.287 AC: 606 AN: 2114

Alfa AF: 0.253 Hom.: 1300

Bravo AF: 0.290

Asia WGS AF: 0.400 AC: 1389 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	1.2
DANN	Benign	0.65
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs11045418; hg19: chr12-8605262;