rs1364063

chr16-69554669-T-C

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 0.345 in 152,122 control chromosomes in the GnomAD database, including 9,737 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 0.34 (9737 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.414 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: 0.345 AC: 52417 AN: 152006 Hom.: 9751 Cov.: 33

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.345 AC: 52410 AN: 152122 Hom.: 9737 Cov.: 33 AF XY: 0.344 AC XY: 25562 AN XY: 74360

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.428

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.350

Alfa AF: 0.398 Hom.: 24083

Bravo AF: 0.331

Asia WGS AF: 0.269 AC: 940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	3.4
Dann	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1364063; hg19: chr16-69588572;