rs33149

Variant names:

• chr12-30824421-A-C
• rs33149
• ENST00000648700.1:n.246+24400A>C

Your query was ambiguous. Multiple possible variants found:

• chr12-30824421-A-C
• chr12-30824421-A-G

Variant summary

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

The ENST00000648700.1(LINC00941):​n.246+24400A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.712 in 151,892 control chromosomes in the GnomAD database, including 39,174 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 0.71 (39174 hom., cov: 30)
• Consequence: LINC00941 ENST00000648700.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.411
• Publications: 4 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=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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.246+24400A>C		intron_variant	Intron 2 of 2
LINC00941	ENST00000754109.1	n.326+24400A>C		intron_variant	Intron 2 of 3
LINC00941	ENST00000754110.1	n.627+24400A>C		intron_variant	Intron 2 of 2
LINC00941	ENST00000754111.1	n.233-1901A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.713 AC: 108157 AN: 151776 Hom.: 39164 Cov.: 30

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.828

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.729

Gnomad NFE AF: 0.742

Gnomad OTH AF: 0.709

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

GnomAD4 genome AF: 0.712 AC: 108204 AN: 151892 Hom.: 39174 Cov.: 30 AF XY: 0.713 AC XY: 52938 AN XY: 74214

African (AFR) AF: 0.651 AC: 26935 AN: 41382

American (AMR) AF: 0.566 AC: 8640 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.747 AC: 2591 AN: 3468

East Asian (EAS) AF: 0.997 AC: 5137 AN: 5154

South Asian (SAS) AF: 0.820 AC: 3947 AN: 4816

European-Finnish (FIN) AF: 0.768 AC: 8111 AN: 10560

Middle Eastern (MID) AF: 0.723 AC: 211 AN: 292

European-Non Finnish (NFE) AF: 0.742 AC: 50381 AN: 67944

Other (OTH) AF: 0.712 AC: 1499 AN: 2106

Alfa AF: 0.725 Hom.: 138758

Bravo AF: 0.694

Asia WGS AF: 0.895 AC: 3110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	4.0
DANN	Benign	0.89
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs33149; hg19: chr12-30977355;