rs4404064

Positions:

• chr16-82019894-G-A
• chr16-82019894-G-C
• chr16-82019894-G-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 0.95 in 152,338 control chromosomes in the GnomAD database, including 68,823 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 0.95 (68823 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.89

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.978 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: 0.950 AC: 144583 AN: 152220 Hom.: 68761 Cov.: 32

Gnomad AFR AF: 0.986

Gnomad AMI AF: 0.956

Gnomad AMR AF: 0.957

Gnomad ASJ AF: 0.900

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.939

Gnomad FIN AF: 0.944

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.928

Gnomad OTH AF: 0.941

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

GnomAD4 genome AF: 0.950 AC: 144705 AN: 152338 Hom.: 68823 Cov.: 32 AF XY: 0.950 AC XY: 70760 AN XY: 74486

Gnomad4 AFR AF: 0.986

Gnomad4 AMR AF: 0.957

Gnomad4 ASJ AF: 0.900

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.938

Gnomad4 FIN AF: 0.944

Gnomad4 NFE AF: 0.928

Gnomad4 OTH AF: 0.942

Alfa AF: 0.930 Hom.: 25533

Bravo AF: 0.953

Asia WGS AF: 0.971 AC: 3378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.014
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4404064; hg19: chr16-82053499;