rs2748249

Positions:

• chr5-150413037-C-A

Variant summary

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

The variant allele was found at a frequency of 0.177 in 1,065,770 control chromosomes in the GnomAD database, including 17,227 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 0.14 (1908 hom., cov: 33)
  • Exomes 𝑓: 0.18 (15319 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.150413037C>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21799 AN: 152118 Hom.: 1898 Cov.: 33

Gnomad AFR AF: 0.0471

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.143

GnomAD4 exome AF: 0.182 AC: 166343 AN: 913534 Hom.: 15319 AF XY: 0.182 AC XY: 79830 AN XY: 439236

Gnomad4 AFR exome AF: 0.0435

Gnomad4 AMR exome AF: 0.158

Gnomad4 ASJ exome AF: 0.151

Gnomad4 EAS exome AF: 0.120

Gnomad4 SAS exome AF: 0.175

Gnomad4 FIN exome AF: 0.209

Gnomad4 NFE exome AF: 0.189

Gnomad4 OTH exome AF: 0.171

GnomAD4 genome AF: 0.143 AC: 21827 AN: 152236 Hom.: 1908 Cov.: 33 AF XY: 0.144 AC XY: 10726 AN XY: 74416

Gnomad4 AFR AF: 0.0470

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.144

Alfa AF: 0.176 Hom.: 2636

Bravo AF: 0.133

Asia WGS AF: 0.143 AC: 498 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	8.8
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2748249; hg19: chr5-149792600;