rs1381102

chr16-63921543-G-A

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 0.41 in 151,946 control chromosomes in the GnomAD database, including 12,962 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 0.41 (12962 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.303

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.45 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: 0.410 AC: 62239 AN: 151828 Hom.: 12953 Cov.: 32

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.410 AC: 62273 AN: 151946 Hom.: 12962 Cov.: 32 AF XY: 0.402 AC XY: 29870 AN XY: 74246

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.365

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.402

Alfa AF: 0.406 Hom.: 9927

Bravo AF: 0.411

Asia WGS AF: 0.348 AC: 1208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.29
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1381102; hg19: chr16-63955447;