rs1364063

Variant names:

• chr16-69554669-T-C
• rs1364063

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;