rs149428

Positions:

• chr16-58634662-G-A
• chr16-58634662-G-C

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 0.3 in 152,020 control chromosomes in the GnomAD database, including 8,164 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 0.30 (8164 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.404 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: 0.300 AC: 45596 AN: 151902 Hom.: 8168 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.0326

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.300 AC: 45584 AN: 152020 Hom.: 8164 Cov.: 32 AF XY: 0.295 AC XY: 21907 AN XY: 74300

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.0326

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.323

Alfa AF: 0.374 Hom.: 19714

Bravo AF: 0.288

Asia WGS AF: 0.127 AC: 442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.18
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs149428; hg19: chr16-58668566;