rs4148382

Variant names:

• chr16-16144637-G-A
• rs4148382

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;