rs67397200

chr19-17290595-C-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 0.264 in 151,996 control chromosomes in the GnomAD database, including 5,594 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 0.26 (5594 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.292 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: 0.264 AC: 40059 AN: 151878 Hom.: 5593 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.261

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.264 AC: 40069 AN: 151996 Hom.: 5594 Cov.: 32 AF XY: 0.259 AC XY: 19213 AN XY: 74306

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.00309

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.260

Alfa AF: 0.289 Hom.: 808

Bravo AF: 0.255

Asia WGS AF: 0.0890 AC: 313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.30
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs67397200; hg19: chr19-17401404;