rs149428

Variant names:

• chr16-58634662-G-A
• rs149428

Your query was ambiguous. Multiple possible variants found:

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

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 0.3 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.140 AC: 5812 AN: 41476

American (AMR) AF: 0.292 AC: 4447 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1159 AN: 3464

East Asian (EAS) AF: 0.0326 AC: 169 AN: 5180

South Asian (SAS) AF: 0.209 AC: 1006 AN: 4820

European-Finnish (FIN) AF: 0.375 AC: 3954 AN: 10554

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27730 AN: 67974

Other (OTH) AF: 0.323 AC: 681 AN: 2108

Alfa AF: 0.361 Hom.: 43967

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs149428; hg19: chr16-58668566;