rs2334004

chr2-238518938-A-Gchr2-238518938-A-T

Variant summary

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

The NR_037809.1(LINC01107):n.1164-6992T>C variant causes a intron, non coding transcript 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 NR_037809.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.736

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01107	NR_037809.1	n.1164-6992T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01107	ENST00000446979.1	n.719-6992T>C		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.0515

Gnomad4 ASJ AF: 0.0135

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.0770

Gnomad4 NFE AF: 0.0205

Gnomad4 OTH AF: 0.104

Alfa AF: 0.109 Hom.: 373

Bravo AF: 0.134

Asia WGS AF: 0.136 AC: 473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	5.3
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2334004; hg19: chr2-239427579;