rs2048741

Positions:

• chr9-117874984-G-A

Variant summary

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

The ENST00000449730.1(ENSG00000231901):​n.127C>T 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 0.419 in 152,030 control chromosomes in the GnomAD database, including 13,436 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 0.42 (13436 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: ENST00000449730.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.482

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376243	XR_001746917.3	n.3581C>T		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000449730.1	n.127C>T		non_coding_transcript_exon_variant	2/4	3
	ENST00000697639.1	n.1053+26829G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63693 AN: 151908 Hom.: 13420 Cov.: 32

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.437

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.419 AC: 63745 AN: 152028 Hom.: 13436 Cov.: 32 AF XY: 0.419 AC XY: 31132 AN XY: 74312

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.439

Alfa AF: 0.425 Hom.: 28300

Bravo AF: 0.427

Asia WGS AF: 0.302 AC: 1050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.38
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2048741; hg19: chr9-120637262;