rs4930939

Variant names:

• chr12-30849551-G-A
• rs4930939
• ENST00000648700.1:n.247-29121G>A

Variant summary

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

The ENST00000648700.1(LINC00941):​n.247-29121G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,184 control chromosomes in the GnomAD database, including 1,819 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 0.14 (1819 hom., cov: 33)
• Consequence: LINC00941 ENST00000648700.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.586
• Publications: 3 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.192 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.247-29121G>A		intron	N/A
	LINC00941	ENST00000754109.1		n.327-29121G>A		intron	N/A
	LINC00941	ENST00000754110.1		n.628-20245G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21371 AN: 152066 Hom.: 1819 Cov.: 33

Gnomad AFR AF: 0.0622

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.0634

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.141 AC: 21387 AN: 152184 Hom.: 1819 Cov.: 33 AF XY: 0.138 AC XY: 10267 AN XY: 74376

African (AFR) AF: 0.0622 AC: 2582 AN: 41542

American (AMR) AF: 0.129 AC: 1968 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 473 AN: 3470

East Asian (EAS) AF: 0.111 AC: 574 AN: 5178

South Asian (SAS) AF: 0.0645 AC: 311 AN: 4822

European-Finnish (FIN) AF: 0.163 AC: 1722 AN: 10556

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13217 AN: 68010

Other (OTH) AF: 0.166 AC: 349 AN: 2108

Alfa AF: 0.180 Hom.: 5232

Bravo AF: 0.134

Asia WGS AF: 0.0990 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.28
DANN	Benign	0.87
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs4930939; hg19: chr12-31002485; COSMIC: COSV66930629;