2-65686953-T-A

Position:

• chr2-65686953-T-A

Variant summary

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

The ENST00000606978.5(LINC02934):​n.456-4829T>A 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 0.264 in 152,134 control chromosomes in the GnomAD database, including 6,576 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 0.26 (6576 hom., cov: 32)
• Consequence: LINC02934 ENST00000606978.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810

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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02934	ENST00000606978.5	n.456-4829T>A		intron_variant, non_coding_transcript_variant		5
LINC02934	ENST00000377977.3	n.863-4829T>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40231 AN: 152014 Hom.: 6577 Cov.: 32

Gnomad AFR AF: 0.0725

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.264 AC: 40227 AN: 152134 Hom.: 6576 Cov.: 32 AF XY: 0.262 AC XY: 19440 AN XY: 74338

Gnomad4 AFR AF: 0.0723

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.299

Alfa AF: 0.297 Hom.: 966

Bravo AF: 0.250

Asia WGS AF: 0.169 AC: 590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.71
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10490612; hg19: chr2-65914087;