rs1544806

Variant names:

• chr16-60659050-C-T
• rs1544806

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 0.788 in 152,126 control chromosomes in the GnomAD database, including 47,363 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 0.79 (47363 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.79
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.801 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: 0.788 AC: 119849 AN: 152008 Hom.: 47335 Cov.: 31

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.802

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.850

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.807

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.788 AC: 119930 AN: 152126 Hom.: 47363 Cov.: 31 AF XY: 0.788 AC XY: 58614 AN XY: 74378

African (AFR) AF: 0.759 AC: 31488 AN: 41500

American (AMR) AF: 0.801 AC: 12242 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.806 AC: 2795 AN: 3468

East Asian (EAS) AF: 0.695 AC: 3574 AN: 5144

South Asian (SAS) AF: 0.683 AC: 3290 AN: 4816

European-Finnish (FIN) AF: 0.850 AC: 8999 AN: 10592

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.807 AC: 54886 AN: 68008

Other (OTH) AF: 0.779 AC: 1645 AN: 2112

Alfa AF: 0.798 Hom.: 6287

Bravo AF: 0.785

Asia WGS AF: 0.688 AC: 2394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.039
DANN	Benign	0.26
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs1544806; hg19: chr16-60692954;