2-66031567-T-C

Position:

• chr2-66031567-T-C

Variant summary

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

The ENST00000606978.5(LINC02934):​n.999+15158T>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 0.923 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 ENST00000606978.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC02934	XR_007086567.1	n.201-40937T>C		intron_variant, non_coding_transcript_variant
LINC02934	XR_007086560.1	n.311-40937T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02934	ENST00000606978.5	n.999+15158T>C		intron_variant, non_coding_transcript_variant		5
LINC02934	ENST00000606556.1	n.142-40937T>C		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.959

Gnomad4 AMR AF: 0.905

Gnomad4 ASJ AF: 0.935

Gnomad4 EAS AF: 0.861

Gnomad4 SAS AF: 0.874

Gnomad4 FIN AF: 0.918

Gnomad4 NFE AF: 0.912

Gnomad4 OTH AF: 0.929

Alfa AF: 0.916 Hom.: 76556

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2699783; hg19: chr2-66258701;