rs67397200

Variant names:

• chr19-17290595-C-G
• rs67397200

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;