rs1424019

chr16-86509435-A-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 0.688 in 152,220 control chromosomes in the GnomAD database, including 37,208 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 0.69 (37208 hom., cov: 36)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.236

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 (EAS) allele frequency at 95% confidence interval = 0.843 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: 0.688 AC: 104663 AN: 152102 Hom.: 37181 Cov.: 36

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.688 AC: 104744 AN: 152220 Hom.: 37208 Cov.: 36 AF XY: 0.692 AC XY: 51536 AN XY: 74422

Gnomad4 AFR AF: 0.497

Gnomad4 AMR AF: 0.804

Gnomad4 ASJ AF: 0.787

Gnomad4 EAS AF: 0.865

Gnomad4 SAS AF: 0.678

Gnomad4 FIN AF: 0.779

Gnomad4 NFE AF: 0.746

Gnomad4 OTH AF: 0.723

Alfa AF: 0.710 Hom.: 4820

Bravo AF: 0.686

Asia WGS AF: 0.755 AC: 2623 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	9.1
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1424019; hg19: chr16-86543041;