2-66031567-T-C

Variant names:

• chr2-66031567-T-C
• rs2699783
• ENST00000606556.1:n.142-40937T>C

Variant summary

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

The ENST00000606556.1(LINC02934):​n.142-40937T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.923 in 152,296 control chromosomes in the GnomAD database, including 64,921 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 0.92 (64921 hom., cov: 33)
• Consequence: LINC02934 ENST00000606556.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800
• Publications: 5 publications found

Genes affected

LINC02934 (HGNC:55913): (long intergenic non-protein coding RNA 2934)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02934	NR_187140.1	n.265-40937T>C		intron_variant	Intron 3 of 5
LINC02934	NR_187141.1	n.273+15158T>C		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02934	ENST00000606556.1	n.142-40937T>C		intron_variant	Intron 1 of 2	2
LINC02934	ENST00000606978.5	n.999+15158T>C		intron_variant	Intron 9 of 9	5
LINC02934	ENST00000737096.1	n.346-52943T>C		intron_variant	Intron 2 of 5
LINC02934	ENST00000737097.1	n.316-18193T>C		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.923 AC: 140444 AN: 152180 Hom.: 64863 Cov.: 33

Gnomad AFR AF: 0.959

Gnomad AMI AF: 0.976

Gnomad AMR AF: 0.905

Gnomad ASJ AF: 0.935

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.874

Gnomad FIN AF: 0.918

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.912

Gnomad OTH AF: 0.929

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

GnomAD4 genome AF: 0.923 AC: 140561 AN: 152296 Hom.: 64921 Cov.: 33 AF XY: 0.920 AC XY: 68486 AN XY: 74474

African (AFR) AF: 0.959 AC: 39869 AN: 41570

American (AMR) AF: 0.905 AC: 13845 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.935 AC: 3245 AN: 3472

East Asian (EAS) AF: 0.861 AC: 4456 AN: 5178

South Asian (SAS) AF: 0.874 AC: 4214 AN: 4820

European-Finnish (FIN) AF: 0.918 AC: 9740 AN: 10614

Middle Eastern (MID) AF: 0.963 AC: 283 AN: 294

European-Non Finnish (NFE) AF: 0.912 AC: 62055 AN: 68032

Other (OTH) AF: 0.929 AC: 1964 AN: 2114

Alfa AF: 0.918 Hom.: 106905

Bravo AF: 0.927

Asia WGS AF: 0.891 AC: 3099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	9.0
DANN	Benign	0.55
PhyloP100		-0.0080

Splicing

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

Other links and lift over

dbSNP: rs2699783; hg19: chr2-66258701;