rs4148382

chr16-16144637-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 0.0723 in 152,258 control chromosomes in the GnomAD database, including 489 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 0.072 (489 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0973 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: 0.0723 AC: 11005 AN: 152140 Hom.: 488 Cov.: 32

Gnomad AFR AF: 0.0197

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.0893

Gnomad ASJ AF: 0.0769

Gnomad EAS AF: 0.0616

Gnomad SAS AF: 0.0412

Gnomad FIN AF: 0.0968

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0993

Gnomad OTH AF: 0.0746

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

GnomAD4 genome AF: 0.0723 AC: 11005 AN: 152258 Hom.: 489 Cov.: 32 AF XY: 0.0701 AC XY: 5220 AN XY: 74428

Gnomad4 AFR AF: 0.0197

Gnomad4 AMR AF: 0.0895

Gnomad4 ASJ AF: 0.0769

Gnomad4 EAS AF: 0.0617

Gnomad4 SAS AF: 0.0402

Gnomad4 FIN AF: 0.0968

Gnomad4 NFE AF: 0.0993

Gnomad4 OTH AF: 0.0734

Alfa AF: 0.0926 Hom.: 997

Bravo AF: 0.0719

Asia WGS AF: 0.0450 AC: 155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	0.89
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4148382; hg19: chr16-16238494;