chr16-55642622-T-A

Variant names:

• chr16-55642622-T-A
• rs35917

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 0.437 in 151,890 control chromosomes in the GnomAD database, including 15,629 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 0.44 (15629 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.62 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: 0.436 AC: 66233 AN: 151772 Hom.: 15591 Cov.: 32

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.437 AC: 66331 AN: 151890 Hom.: 15629 Cov.: 32 AF XY: 0.433 AC XY: 32118 AN XY: 74230

African (AFR) AF: 0.626 AC: 25909 AN: 41386

American (AMR) AF: 0.407 AC: 6213 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1199 AN: 3468

East Asian (EAS) AF: 0.406 AC: 2096 AN: 5164

South Asian (SAS) AF: 0.321 AC: 1549 AN: 4820

European-Finnish (FIN) AF: 0.340 AC: 3569 AN: 10512

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.360 AC: 24479 AN: 67952

Other (OTH) AF: 0.403 AC: 850 AN: 2110

Alfa AF: 0.412 Hom.: 1688

Bravo AF: 0.452

Asia WGS AF: 0.395 AC: 1372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.69
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs35917; hg19: chr16-55676534;