chr2-238518938-A-G

Variant names:

• chr2-238518938-A-G
• rs2334004
• ENST00000446979.1:n.719-6992T>C

Variant summary

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

The ENST00000446979.1(LINC01107):​n.719-6992T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,156 control chromosomes in the GnomAD database, including 2,818 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 0.13 (2818 hom., cov: 32)
• Consequence: LINC01107 ENST00000446979.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.736
• Publications: 4 publications found

Genes affected

LINC01107 (HGNC:49229): (long intergenic non-protein coding RNA 1107)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000446979.1. 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
	LINC01107	NR_037809.1		n.1164-6992T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01107	ENST00000446979.1	TSL:2	n.719-6992T>C		intron	N/A
	LINC01107	ENST00000748485.1		n.347-10017T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19264 AN: 152038 Hom.: 2812 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.0264

Gnomad AMR AF: 0.0516

Gnomad ASJ AF: 0.0135

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0770

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0205

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.127 AC: 19295 AN: 152156 Hom.: 2818 Cov.: 32 AF XY: 0.128 AC XY: 9532 AN XY: 74386

African (AFR) AF: 0.353 AC: 14612 AN: 41452

American (AMR) AF: 0.0515 AC: 788 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0135 AC: 47 AN: 3470

East Asian (EAS) AF: 0.151 AC: 783 AN: 5174

South Asian (SAS) AF: 0.123 AC: 591 AN: 4820

European-Finnish (FIN) AF: 0.0770 AC: 817 AN: 10616

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0205 AC: 1394 AN: 68014

Other (OTH) AF: 0.104 AC: 218 AN: 2106

Alfa AF: 0.0840 Hom.: 486

Bravo AF: 0.134

Asia WGS AF: 0.136 AC: 473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.3
DANN	Benign	0.58
PhyloP100		0.74

Splicing

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

Other links and lift over

dbSNP: rs2334004; hg19: chr2-239427579;