rs16920160

Variant names:

• chr8-54395731-G-A
• rs16920160

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 0.0486 in 152,232 control chromosomes in the GnomAD database, including 241 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 0.049 (241 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470
• Publications: 3 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 = 0.071 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: 0.0487 AC: 7405 AN: 152114 Hom.: 240 Cov.: 32

Gnomad AFR AF: 0.0114

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0474

Gnomad ASJ AF: 0.0481

Gnomad EAS AF: 0.0773

Gnomad SAS AF: 0.0294

Gnomad FIN AF: 0.0961

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0641

Gnomad OTH AF: 0.0373

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

GnomAD4 genome AF: 0.0486 AC: 7405 AN: 152232 Hom.: 241 Cov.: 32 AF XY: 0.0498 AC XY: 3706 AN XY: 74436

African (AFR) AF: 0.0114 AC: 474 AN: 41558

American (AMR) AF: 0.0475 AC: 726 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0481 AC: 167 AN: 3472

East Asian (EAS) AF: 0.0773 AC: 400 AN: 5176

South Asian (SAS) AF: 0.0301 AC: 145 AN: 4820

European-Finnish (FIN) AF: 0.0961 AC: 1019 AN: 10600

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0641 AC: 4361 AN: 68002

Other (OTH) AF: 0.0364 AC: 77 AN: 2114

Alfa AF: 0.0550 Hom.: 403

Bravo AF: 0.0446

Asia WGS AF: 0.0350 AC: 123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.70
PhyloP100		-0.047

Splicing

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

Other links and lift over

dbSNP: rs16920160; hg19: chr8-55308291;