16-20098331-G-A

Variant names:

• chr16-20098331-G-A
• rs11642377

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 0.219 in 152,078 control chromosomes in the GnomAD database, including 3,883 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 0.22 (3883 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460
• Publications: 4 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 (EAS) allele frequency at 95% confidence interval = 0.256 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: 0.219 AC: 33328 AN: 151960 Hom.: 3883 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.219 AC: 33343 AN: 152078 Hom.: 3883 Cov.: 32 AF XY: 0.222 AC XY: 16495 AN XY: 74328

African (AFR) AF: 0.139 AC: 5751 AN: 41498

American (AMR) AF: 0.234 AC: 3574 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 616 AN: 3468

East Asian (EAS) AF: 0.268 AC: 1383 AN: 5164

South Asian (SAS) AF: 0.232 AC: 1119 AN: 4816

European-Finnish (FIN) AF: 0.299 AC: 3160 AN: 10568

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16882 AN: 67970

Other (OTH) AF: 0.210 AC: 443 AN: 2114

Alfa AF: 0.232 Hom.: 13271

Bravo AF: 0.213

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.23
PhyloP100		-0.046

Splicing

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

Other links and lift over

dbSNP: rs11642377; hg19: chr16-20109653;