2-135741596-G-T

Position:

• chr2-135741596-G-T

Variant summary

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

The NR_163478.1(LOC107985946):​n.1049C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 325,492 control chromosomes in the GnomAD database, including 63,511 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 0.53 (25504 hom., cov: 33)
  • Exomes 𝑓: 0.64 (38007 hom.)
• Consequence: LOC107985946 NR_163478.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226

Genes affected

LOC107985946 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985946	NR_163478.1	n.1049C>A		non_coding_transcript_exon_variant	1/1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80260 AN: 152044 Hom.: 25502 Cov.: 33

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.783

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.481

GnomAD4 exome AF: 0.637 AC: 110447 AN: 173330 Hom.: 38007 Cov.: 1 AF XY: 0.627 AC XY: 55910 AN XY: 89218

Gnomad4 AFR exome AF: 0.220

Gnomad4 AMR exome AF: 0.462

Gnomad4 ASJ exome AF: 0.372

Gnomad4 EAS exome AF: 0.438

Gnomad4 SAS exome AF: 0.430

Gnomad4 FIN exome AF: 0.736

Gnomad4 NFE exome AF: 0.719

Gnomad4 OTH exome AF: 0.594

GnomAD4 genome AF: 0.527 AC: 80264 AN: 152162 Hom.: 25504 Cov.: 33 AF XY: 0.519 AC XY: 38587 AN XY: 74392

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.378

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.733

Gnomad4 NFE AF: 0.732

Gnomad4 OTH AF: 0.476

Alfa AF: 0.643 Hom.: 49745

Bravo AF: 0.496

Asia WGS AF: 0.393 AC: 1368 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	2.2
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1438307; hg19: chr2-136499166;