16-55507128-G-T

Variant names:

• chr16-55507128-G-T
• rs1861320

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 0.368 in 151,958 control chromosomes in the GnomAD database, including 11,224 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 0.37 (11224 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.665
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55887 AN: 151842 Hom.: 11219 Cov.: 31

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.368 AC: 55907 AN: 151958 Hom.: 11224 Cov.: 31 AF XY: 0.364 AC XY: 27070 AN XY: 74284

African (AFR) AF: 0.199 AC: 8267 AN: 41446

American (AMR) AF: 0.442 AC: 6751 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1391 AN: 3458

East Asian (EAS) AF: 0.232 AC: 1195 AN: 5142

South Asian (SAS) AF: 0.320 AC: 1543 AN: 4820

European-Finnish (FIN) AF: 0.399 AC: 4217 AN: 10556

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 31014 AN: 67956

Other (OTH) AF: 0.390 AC: 823 AN: 2108

Alfa AF: 0.415 Hom.: 8116

Bravo AF: 0.365

Asia WGS AF: 0.236 AC: 820 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
DANN	Benign	0.79
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs1861320; hg19: chr16-55541040;