2-149840634-A-G

Variant names:

• chr2-149840634-A-G
• rs11889862
• ENST00000295052.3:n.1302+16817T>C

Variant summary

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

The ENST00000295052.3(LINC01931):​n.1302+16817T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.733 in 152,066 control chromosomes in the GnomAD database, including 41,261 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 0.73 (41261 hom., cov: 32)
• Consequence: LINC01931 ENST00000295052.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388
• Publications: 10 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000295052.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MMADHC-DT	NR_110240.1		n.536-7275A>G		intron	N/A
	LINC01931	NR_145421.1		n.1302+16817T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01931	ENST00000295052.3	TSL:2	n.1302+16817T>C		intron	N/A
	LINC01931	ENST00000433174.1	TSL:2	n.235+16817T>C		intron	N/A
	MMADHC-DT	ENST00000449714.3	TSL:2	n.611-7275A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.733 AC: 111448 AN: 151948 Hom.: 41234 Cov.: 32

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.733 AC: 111525 AN: 152066 Hom.: 41261 Cov.: 32 AF XY: 0.730 AC XY: 54251 AN XY: 74326

African (AFR) AF: 0.680 AC: 28198 AN: 41490

American (AMR) AF: 0.627 AC: 9563 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.773 AC: 2685 AN: 3472

East Asian (EAS) AF: 0.639 AC: 3298 AN: 5158

South Asian (SAS) AF: 0.747 AC: 3602 AN: 4824

European-Finnish (FIN) AF: 0.754 AC: 7967 AN: 10560

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.791 AC: 53812 AN: 67988

Other (OTH) AF: 0.725 AC: 1535 AN: 2116

Alfa AF: 0.770 Hom.: 154647

Bravo AF: 0.719

Asia WGS AF: 0.729 AC: 2530 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.30
DANN	Benign	0.58
PhyloP100		-0.39

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11889862;

hg19: chr2-150697148;