2-151354289-A-T

Position:

• chr2-151354289-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_110248.1(LOC101929319):​n.307-14890T>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 0.25 in 152,146 control chromosomes in the GnomAD database, including 5,412 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 0.25 (5412 hom., cov: 32)
• Consequence: LOC101929319 NR_110248.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.67

Genes affected

LOC101929319 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101929319	NR_110248.1	n.307-14890T>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.250 AC: 38029 AN: 152028 Hom.: 5399 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.250 AC: 38063 AN: 152146 Hom.: 5412 Cov.: 32 AF XY: 0.248 AC XY: 18432 AN XY: 74380

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.328

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.288

Alfa AF: 0.272 Hom.: 715

Bravo AF: 0.239

Asia WGS AF: 0.376 AC: 1304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	16
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2342910; hg19: chr2-152210803;