chr2-149833000-C-T

Variant names:

• chr2-149833000-C-T
• rs4132253
• ENST00000295052.3:n.1302+24451G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000295052.3(LINC01931):​n.1302+24451G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 151,944 control chromosomes in the GnomAD database, including 2,176 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 0.15 (2176 hom., cov: 32)
• Consequence: LINC01931 ENST00000295052.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700

Genes affected

LINC01931 (HGNC:52743): (long intergenic non-protein coding RNA 1931)

MMADHC-DT (HGNC:41087): (MMADHC divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MMADHC-DT	NR_110240.1	n.536-14909C>T		intron_variant	Intron 2 of 2
LINC01931	NR_145421.1	n.1302+24451G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01931	ENST00000295052.3	n.1302+24451G>A		intron_variant	Intron 2 of 4	2
LINC01931	ENST00000433174.1	n.236-16216G>A		intron_variant	Intron 1 of 1	2
MMADHC-DT	ENST00000449714.2	n.611-14909C>T		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22805 AN: 151826 Hom.: 2172 Cov.: 32

Gnomad AFR AF: 0.0671

Gnomad AMI AF: 0.0725

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.150 AC: 22808 AN: 151944 Hom.: 2176 Cov.: 32 AF XY: 0.152 AC XY: 11274 AN XY: 74248

Gnomad4 AFR AF: 0.0671

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.162

Alfa AF: 0.0979 Hom.: 245

Bravo AF: 0.153

Asia WGS AF: 0.316 AC: 1095 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.6
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4132253; hg19: chr2-150689514;