rs2742946

Positions:

• chr1-23559582-T-C

Variant summary

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

The XR_007065537.1(LOC124903876):​n.282+7487T>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 0.442 in 913,402 control chromosomes in the GnomAD database, including 91,309 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 0.43 (14515 hom., cov: 34)
  • Exomes 𝑓: 0.44 (76794 hom.)
• Consequence: LOC124903876 XR_007065537.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.548

Genes affected

LOC124903876 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.562 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903876	XR_007065537.1	n.282+7487T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65741 AN: 152126 Hom.: 14523 Cov.: 34

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.468

GnomAD4 exome AF: 0.444 AC: 338106 AN: 761158 Hom.: 76794 Cov.: 10 AF XY: 0.443 AC XY: 169198 AN XY: 382214

Gnomad4 AFR exome AF: 0.360

Gnomad4 AMR exome AF: 0.396

Gnomad4 ASJ exome AF: 0.516

Gnomad4 EAS exome AF: 0.574

Gnomad4 SAS exome AF: 0.361

Gnomad4 FIN exome AF: 0.435

Gnomad4 NFE exome AF: 0.447

Gnomad4 OTH exome AF: 0.444

GnomAD4 genome AF: 0.432 AC: 65748 AN: 152244 Hom.: 14515 Cov.: 34 AF XY: 0.430 AC XY: 32044 AN XY: 74460

Gnomad4 AFR AF: 0.370

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.509

Gnomad4 EAS AF: 0.579

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.437

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.467

Alfa AF: 0.452 Hom.: 2791

Bravo AF: 0.433

Asia WGS AF: 0.426 AC: 1482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	18
DANN	Benign	0.41

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2742946; hg19: chr1-23886073;