chr16-56637784-T-C

Variant names:

• chr16-56637784-T-C
• rs1846692

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 0.699 in 152,120 control chromosomes in the GnomAD database, including 38,055 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 0.70 (38055 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.700 AC: 106346 AN: 152004 Hom.: 38044 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.703

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

GnomAD4 genome AF: 0.699 AC: 106396 AN: 152120 Hom.: 38055 Cov.: 32 AF XY: 0.700 AC XY: 52032 AN XY: 74374

African (AFR) AF: 0.565 AC: 23429 AN: 41474

American (AMR) AF: 0.734 AC: 11208 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.691 AC: 2399 AN: 3472

East Asian (EAS) AF: 0.497 AC: 2571 AN: 5170

South Asian (SAS) AF: 0.633 AC: 3054 AN: 4822

European-Finnish (FIN) AF: 0.831 AC: 8808 AN: 10600

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.774 AC: 52613 AN: 67986

Other (OTH) AF: 0.699 AC: 1476 AN: 2112

Alfa AF: 0.744 Hom.: 9251

Bravo AF: 0.687

Asia WGS AF: 0.594 AC: 2067 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.64
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs1846692; hg19: chr16-56671696;