2-100605168-A-G

Variant names:

• chr2-100605168-A-G
• rs4261746
• ENST00000424342.2:n.123+1278A>G

Variant summary

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

The ENST00000424342.2(LINC01849):​n.123+1278A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 151,966 control chromosomes in the GnomAD database, including 38,053 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 0.69 (38053 hom., cov: 31)
• Consequence: LINC01849 ENST00000424342.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152

Genes affected

LINC01849 (HGNC:52665): (long intergenic non-protein coding RNA 1849)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01849	NR_146956.1	n.152+1278A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01849	ENST00000424342.2	n.123+1278A>G		intron_variant	Intron 1 of 2	3
LINC01849	ENST00000656519.1	n.139+1278A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104548 AN: 151846 Hom.: 37984 Cov.: 31

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.610

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.689 AC: 104675 AN: 151966 Hom.: 38053 Cov.: 31 AF XY: 0.697 AC XY: 51749 AN XY: 74244

African (AFR) AF: 0.883 AC: 36635 AN: 41474

American (AMR) AF: 0.721 AC: 10994 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1895 AN: 3468

East Asian (EAS) AF: 0.998 AC: 5171 AN: 5180

South Asian (SAS) AF: 0.870 AC: 4191 AN: 4818

European-Finnish (FIN) AF: 0.615 AC: 6469 AN: 10526

Middle Eastern (MID) AF: 0.618 AC: 178 AN: 288

European-Non Finnish (NFE) AF: 0.548 AC: 37260 AN: 67948

Other (OTH) AF: 0.657 AC: 1386 AN: 2110

Alfa AF: 0.573 Hom.: 12648

Bravo AF: 0.706

Asia WGS AF: 0.917 AC: 3182 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4261746; hg19: chr2-101221630;