rs1023446

Positions:

• chr16-19402664-C-T

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 0.584 in 151,922 control chromosomes in the GnomAD database, including 26,270 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 0.58 (26270 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.7 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: 0.584 AC: 88646 AN: 151804 Hom.: 26248 Cov.: 31

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.584 AC: 88709 AN: 151922 Hom.: 26270 Cov.: 31 AF XY: 0.585 AC XY: 43427 AN XY: 74244

Gnomad4 AFR AF: 0.510

Gnomad4 AMR AF: 0.631

Gnomad4 ASJ AF: 0.548

Gnomad4 EAS AF: 0.578

Gnomad4 SAS AF: 0.720

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.611

Gnomad4 OTH AF: 0.572

Alfa AF: 0.578 Hom.: 4804

Bravo AF: 0.580

Asia WGS AF: 0.639 AC: 2223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.4
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1023446; hg19: chr16-19413986;