rs10492243

Variant names:

• chr12-30830616-T-C
• rs10492243
• ENST00000648700.1:n.246+30595T>C

Variant summary

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

The ENST00000648700.1(LINC00941):​n.246+30595T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 151,970 control chromosomes in the GnomAD database, including 2,667 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 (2667 hom., cov: 32)
• Consequence: LINC00941 ENST00000648700.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32
• Publications: 10 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648700.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00941	ENST00000648700.1		n.246+30595T>C		intron	N/A
	LINC00941	ENST00000754109.1		n.326+30595T>C		intron	N/A
	LINC00941	ENST00000754110.1		n.627+30595T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24592 AN: 151852 Hom.: 2662 Cov.: 32

Gnomad AFR AF: 0.0646

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.162 AC: 24601 AN: 151970 Hom.: 2667 Cov.: 32 AF XY: 0.166 AC XY: 12361 AN XY: 74284

African (AFR) AF: 0.0644 AC: 2671 AN: 41454

American (AMR) AF: 0.366 AC: 5594 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 634 AN: 3468

East Asian (EAS) AF: 0.195 AC: 1007 AN: 5158

South Asian (SAS) AF: 0.209 AC: 1003 AN: 4798

European-Finnish (FIN) AF: 0.140 AC: 1477 AN: 10548

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.172 AC: 11694 AN: 67964

Other (OTH) AF: 0.184 AC: 388 AN: 2108

Alfa AF: 0.183 Hom.: 4555

Bravo AF: 0.174

Asia WGS AF: 0.179 AC: 621 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.8
DANN	Benign	0.67
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs10492243; hg19: chr12-30983550;