12-30858657-T-C

Variant names:

• chr12-30858657-T-C
• rs581642
• ENST00000648700.1:n.247-20015T>C

Variant summary

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

The ENST00000648700.1(LINC00941):​n.247-20015T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 152,036 control chromosomes in the GnomAD database, including 23,082 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 0.55 (23082 hom., cov: 33)
• Consequence: LINC00941 ENST00000648700.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990
• Publications: 2 publications found

Genes affected

LINC00941 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.61 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
LINC00941	ENST00000648700.1	n.247-20015T>C		intron_variant	Intron 2 of 2
LINC00941	ENST00000754109.1	n.327-20015T>C		intron_variant	Intron 2 of 3
LINC00941	ENST00000754110.1	n.628-11139T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83229 AN: 151918 Hom.: 23075 Cov.: 33

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.572

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.691

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.548 AC: 83268 AN: 152036 Hom.: 23082 Cov.: 33 AF XY: 0.549 AC XY: 40801 AN XY: 74304

African (AFR) AF: 0.469 AC: 19431 AN: 41466

American (AMR) AF: 0.620 AC: 9477 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 2312 AN: 3472

East Asian (EAS) AF: 0.600 AC: 3100 AN: 5168

South Asian (SAS) AF: 0.599 AC: 2886 AN: 4820

European-Finnish (FIN) AF: 0.510 AC: 5373 AN: 10540

Middle Eastern (MID) AF: 0.685 AC: 200 AN: 292

European-Non Finnish (NFE) AF: 0.570 AC: 38764 AN: 67982

Other (OTH) AF: 0.571 AC: 1203 AN: 2108

Alfa AF: 0.567 Hom.: 13026

Bravo AF: 0.555

Asia WGS AF: 0.535 AC: 1860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.4
DANN	Benign	0.72
PhyloP100		-0.099

Splicing

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

Other links and lift over

dbSNP: rs581642; hg19: chr12-31011591;