12-30871083-C-G

Variant names:

• chr12-30871083-C-G
• rs256726
• ENST00000648700.1:n.247-7589C>G

Variant summary

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

The ENST00000648700.1(LINC00941):​n.247-7589C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,070 control chromosomes in the GnomAD database, including 8,844 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 0.33 (8844 hom., cov: 32)
• Consequence: LINC00941 ENST00000648700.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.208
• Publications: 0 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.458 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00941	ENST00000648700.1		n.247-7589C>G		intron	N/A
	LINC00941	ENST00000754109.1		n.327-7589C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49433 AN: 151952 Hom.: 8831 Cov.: 32

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.325 AC: 49475 AN: 152070 Hom.: 8844 Cov.: 32 AF XY: 0.324 AC XY: 24051 AN XY: 74334

African (AFR) AF: 0.452 AC: 18750 AN: 41460

American (AMR) AF: 0.247 AC: 3772 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1204 AN: 3472

East Asian (EAS) AF: 0.473 AC: 2441 AN: 5158

South Asian (SAS) AF: 0.282 AC: 1364 AN: 4832

European-Finnish (FIN) AF: 0.237 AC: 2510 AN: 10570

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18377 AN: 67984

Other (OTH) AF: 0.320 AC: 675 AN: 2112

Alfa AF: 0.293 Hom.: 877

Bravo AF: 0.336

Asia WGS AF: 0.371 AC: 1288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.16
DANN	Benign	0.54
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs256726; hg19: chr12-31024017;