rs7246045

Positions:

• chr19-49042825-T-G

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 0.00887 in 629,238 control chromosomes in the GnomAD database, including 244 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 0.027 (184 hom., cov: 32)
  • Exomes 𝑓: 0.0030 (60 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.49042825T>G		intergenic_region
LOC100287453		n.49042825T>G		intragenic_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0272 AC: 4135 AN: 152010 Hom.: 182 Cov.: 32

Gnomad AFR AF: 0.0938

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0112

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00213

Gnomad SAS AF: 0.00166

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000309

Gnomad OTH AF: 0.0211

GnomAD4 exome AF: 0.00300 AC: 1429 AN: 477110 Hom.: 60 AF XY: 0.00259 AC XY: 642 AN XY: 247920

Gnomad4 AFR exome AF: 0.0855

Gnomad4 AMR exome AF: 0.00519

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000586

Gnomad4 SAS exome AF: 0.00107

Gnomad4 FIN exome AF: 0.0000767

Gnomad4 NFE exome AF: 0.000152

Gnomad4 OTH exome AF: 0.00608

GnomAD4 genome AF: 0.0273 AC: 4155 AN: 152128 Hom.: 184 Cov.: 32 AF XY: 0.0267 AC XY: 1989 AN XY: 74392

Gnomad4 AFR AF: 0.0940

Gnomad4 AMR AF: 0.0112

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.00213

Gnomad4 SAS AF: 0.00166

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000309

Gnomad4 OTH AF: 0.0208

Alfa AF: 0.0240 Hom.: 17

Bravo AF: 0.0313

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7246045; hg19: chr19-49546082;