10-120723599-A-T

Position:

• chr10-120723599-A-T

Variant summary

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

The ENST00000659883.1(LINC02930):​n.402+87450A>T 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 0.315 in 151,938 control chromosomes in the GnomAD database, including 7,825 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 0.32 (7825 hom., cov: 31)
• Consequence: LINC02930 ENST00000659883.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.641

Genes affected

LINC02930 (HGNC:55821): (long intergenic non-protein coding RNA 2930)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02930	XR_002957103.2	n.400+87450A>T		intron_variant, non_coding_transcript_variant
LINC02930	XR_007062314.1	n.1110+87450A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02930	ENST00000659883.1	n.402+87450A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47894 AN: 151820 Hom.: 7817 Cov.: 31

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.315 AC: 47928 AN: 151938 Hom.: 7825 Cov.: 31 AF XY: 0.320 AC XY: 23754 AN XY: 74258

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.334

Alfa AF: 0.279 Hom.: 719

Bravo AF: 0.330

Asia WGS AF: 0.398 AC: 1386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.98
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10510079; hg19: chr10-122483111;