rs4148382

Variant names:

• chr16-16144637-G-A
• rs4148382

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0197 AC: 817 AN: 41556

American (AMR) AF: 0.0895 AC: 1369 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0769 AC: 267 AN: 3472

East Asian (EAS) AF: 0.0617 AC: 320 AN: 5186

South Asian (SAS) AF: 0.0402 AC: 194 AN: 4826

European-Finnish (FIN) AF: 0.0968 AC: 1025 AN: 10594

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0993 AC: 6755 AN: 68016

Other (OTH) AF: 0.0734 AC: 155 AN: 2112

Alfa AF: 0.0884 Hom.: 1456

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
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs4148382; hg19: chr16-16238494;