2-238550962-C-T

Variant names:

• chr2-238550962-C-T
• rs10209564
• ENST00000446979.1:n.718+449G>A

Variant summary

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

The ENST00000446979.1(LINC01107):​n.718+449G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 151,758 control chromosomes in the GnomAD database, including 8,956 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 0.28 (8956 hom., cov: 32)
• Consequence: LINC01107 ENST00000446979.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01107	NR_037809.1	n.1163+449G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01107	ENST00000446979.1	n.718+449G>A		intron_variant	Intron 2 of 2	2
LINC01107	ENST00000748485.1	n.346+449G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.277 AC: 41987 AN: 151638 Hom.: 8924 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.0644

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.0766

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.277 AC: 42072 AN: 151758 Hom.: 8956 Cov.: 32 AF XY: 0.274 AC XY: 20280 AN XY: 74126

African (AFR) AF: 0.597 AC: 24697 AN: 41336

American (AMR) AF: 0.148 AC: 2257 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.0766 AC: 266 AN: 3472

East Asian (EAS) AF: 0.250 AC: 1289 AN: 5158

South Asian (SAS) AF: 0.151 AC: 725 AN: 4810

European-Finnish (FIN) AF: 0.212 AC: 2235 AN: 10536

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 10007 AN: 67894

Other (OTH) AF: 0.240 AC: 505 AN: 2106

Alfa AF: 0.144 Hom.: 1139

Bravo AF: 0.288

Asia WGS AF: 0.208 AC: 725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.8
DANN	Benign	0.67
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs10209564; hg19: chr2-239459603;