rs907100

Variant names:

• chr2-238654938-G-C
• rs907100
• ENST00000653335.1:n.193+84122G>C

Your query was ambiguous. Multiple possible variants found:

• chr2-238654938-G-C
• chr2-238654938-G-T

Variant summary

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

The ENST00000653335.1(LINC01937):​n.193+84122G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 152,094 control chromosomes in the GnomAD database, including 23,576 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 0.54 (23576 hom., cov: 33)
• Consequence: LINC01937 ENST00000653335.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400

Genes affected

LINC01937 (HGNC:52760): (long intergenic non-protein coding RNA 1937)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01937	ENST00000653335.1	n.193+84122G>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81932 AN: 151976 Hom.: 23547 Cov.: 33

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.539 AC: 82012 AN: 152094 Hom.: 23576 Cov.: 33 AF XY: 0.538 AC XY: 40029 AN XY: 74344

Gnomad4 AFR AF: 0.763

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.468

Gnomad4 EAS AF: 0.544

Gnomad4 SAS AF: 0.579

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.446

Gnomad4 OTH AF: 0.512

Alfa AF: 0.317 Hom.: 709

Bravo AF: 0.547

Asia WGS AF: 0.591 AC: 2051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs907100; hg19: chr2-239563579;