rs17318596

chr19-41431190-G-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP3 BP6 BA1

The variant allele was found at a frequency of 0.374 in 518,682 control chromosomes in the GnomAD database, including 38,178 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.33 (9188 hom., cov: 32)
  • Exomes 𝑓: 0.39 (28990 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.48

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• PP3: BayesDel_noAF computational evidence supports a deleterious effect, 0.15
• BP6: Variant 19-41431190-G-A is Benign according to our data. Variant chr19-41431190-G-A is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50488 AN: 151862 Hom.: 9174 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.347

GnomAD3 exomes AF: 0.398 AC: 91165 AN: 229234 Hom.: 19084 AF XY: 0.396 AC XY: 50181 AN XY: 126712

Gnomad AFR exome AF: 0.191

Gnomad AMR exome AF: 0.507

Gnomad ASJ exome AF: 0.374

Gnomad EAS exome AF: 0.565

Gnomad SAS exome AF: 0.402

Gnomad FIN exome AF: 0.341

Gnomad NFE exome AF: 0.370

Gnomad OTH exome AF: 0.377

GnomAD4 exome AF: 0.391 AC: 143302 AN: 366702 Hom.: 28990 Cov.: 0 AF XY: 0.392 AC XY: 82463 AN XY: 210264

Gnomad4 AFR exome AF: 0.196

Gnomad4 AMR exome AF: 0.506

Gnomad4 ASJ exome AF: 0.374

Gnomad4 EAS exome AF: 0.559

Gnomad4 SAS exome AF: 0.409

Gnomad4 FIN exome AF: 0.340

Gnomad4 NFE exome AF: 0.370

Gnomad4 OTH exome AF: 0.369

GnomAD4 genome AF: 0.333 AC: 50537 AN: 151980 Hom.: 9188 Cov.: 32 AF XY: 0.336 AC XY: 24959 AN XY: 74270

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.423

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.560

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.350

Alfa AF: 0.372 Hom.: 19415

Bravo AF: 0.334

Asia WGS AF: 0.465 AC: 1619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Pathogenic	0.15
Cadd	Benign	0.045
Dann	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17318596; hg19: chr19-41937095; COSMIC: COSV55729421;